And the positional relationship between the intervals, so you can always find them regardless of what Key you are in and all over the neck.
Hi Joshua,
Others here are talking about theory, but the skill you are asking about isn’t necessarily about theory.
Have a look at the Re-Active Listening lesson in the Major Scale Maestro module in Grade 4. It isn’t advanced if you already know major scale pattern 1 and if you don’t know it, the module starts with learning the pattern.
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I guess I don’t make my point very clear. I was trying to say it’s easier to hear C to E as a major 3rd than it is to hear them as the notes C and E.
If you play these to notes most people could hear the major 3rd relationship but not very many prople would say the first note is C and the second note is E. But if you know the first note is C you should know the second is E not because you hear a E note but you hear the major 3rd interval.
Yes that makes sense 
If you don’t already have perfect pitch (which I assume is the case), then you’re not very likely to be able to name a random note you hear like “it’s an Eb” or “it’s an A#”.
I think it would be more efficient to focus on the context of what you play, knowing what key you’re playing in, and then finding the right note(s) based on that.
It is quite advanced indeed.
But, I think you are asking the question from a flawed perspective.
If you are thinking this … “I need a C# to go with the chord being played” … I think it fair to assume that you are describing a context in which you are playing single notes over chords, in other words playing a melody or a lead part or a solo or something improvised. That C# note must then be just one note of many - either the first, the last or somewhere in the middle of a group of other different notes played over the same or different chords.
Example.
C# is a note within the A major chord.
You are describing a situation of playing over an A major chord and thinking “I want to play C# now. Where can I find C#?”
If you switch your perspective to one of thinking “I want to play the major 3rd of the chord now” then your ability to do so will be enhanced.
That might seem like a subtle switch but it is vital in allowing you to think for any chord in any key over any progression at any time.
How?
CAGED and triads.
The chord is A major. Where can you find that chord when thinking of CAGED shapes?
The triad is A, C#, E. Where can you find A triads on the guitar when thinking of three adjacent strings?
On any given three adjacent strings, there are only three triad shapes for major triads. Each shape has each of the chord tones on a different string. C# is the major 3rd of an A major triad. It can be found as shown here:
Triad knowledge includes knowing which of the three notes within a triad shape is the root, the 3rd and the 5th. For minor triads that would be root, b3rd and 5th.
The note you mention, C#, could equally be the 5th of an F# minor chord. Then your thinking would focus on F# minor triads and knowing where the 5th is.
Remember that these triads are subsets of bigger CAGED chords. Remember also that these triads sit within scale patterns. Shapes and patterns and CAGED come to the rescue again! 
Yes, learn the notes on the fretboard - over time, not in a hurried manner. But for lead guitar playing and wishing to target certain notes tied in with underlying chords, think of the note quality and where it sits within shapes and patterns.
You could start here perhaps. Triads & Soloing & Targeting Chord Tones Part 1 - getting started
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Hi Joshua, given that I’m not probably understanding properly what you’re asking, and that maybe that is too advanced for me to understand, what David says makes much sense to me; if you suppose to be tone challenged then you shouldn’t be further complicate it with theory: just start from direct experience, grab your guitar and try to work out easy melodies by ear, IMHO, as “simple” as that…naming the notes is very good to me, probably not ideal but it helped me a lot…one thing I should mention is: since it’s not something that comes easy to me I stay only on the first position and that makes things way easier.
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major Should that not be the minor triad shape as per your diagram Richard ?
Fixed. Thanks Toby.
C# is the 5th of F#m and F# triads. I chose minor on purpose to be able to show different shapes for minor triads in the diagrams.
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Silvia, you don’t have to know major scale pattern1 for Re-Active Listening. The first Re-Active Listening lesson is in module 11 and uses the open position.
You are quite right about finding melodies by ear. It’s a great exercise. I sometimes just play around with the scale, not trying to find a melody, and I’ll hear something that sounds familiar and then see if I can find more of that melody.
Re-Active Listening is all about finding chord tones…BUT it’s about finding them by ear…NOT about finding them by using the theory knowledge. Knowing the theory is obviously good but as Justin says in the Grade4 re-active lesson, you simply don’t have time to think about all the theory when you are actually playing.
Re-Active Listening is by far the best lesson, the most influential lesson that I’ve found so far in amongst all Justin’s great lessons.
I don’t do enough of it but what I’ve done with it so far has shown me what the possibilities are or could be. I think it’s HUGE.
That said, I’m not sure whether it’s this re-active thing that Joshua is looking for or something else.
Wow, glad to start a big conversation. I guess I hadn’t thought to far through this. Of course it would be lovely to have perfect pitch and name the note by sound alone, but that would happen in this life.
I guess what I am looking for are what Richard posted and a bit of just tone recognition, such that I know about where I am on the fretboard a little.
I have struggled with figuring out simple melodies on my own because my “aural memory “ for lack of a better term this early in the morning, is having a hard time figuring out where even to start.
I find it a little encumbering that although I know where notes are, cords are and can play some songs, if someone were to play a note, I feel like I would struggle to figure out where to even start to look for it.
I think I will go back to the reactive listening, triads and intervals.
I have soooooo much I need to do!
Here’s a simple exercise that maybe worth trying. Record yourself playing for example a couple of individual notes on the low E string. Put the recording aside until it’s out of your memory. Then play the note and hum the note your hearing. Then pick up your guitar and play a note on the low E string. Is the note you played higher or lower? Play another note and ask the same question until you match the note.
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Lovely, maybe. Useful? Not as much as you might think.
Knowing the function of a note in the context of a song is, generally, far more useful than knowing the actual name of the note.
Cheers,
Keith
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Perfect pitch - being able to hear and name a single note - is a gift that very few people have.
Relative pitch - hearing 2 notes and naming the interval between them is something that can be learned and developed with ear training.
I wouldn’t worry about perfect pitch.
We can all improve relative pitch. Re-active listening is a part of ear training.
Grade 2, Module 11…Joshua this is the lesson for you! Thanks David for suggesting it, I think that while arranging my little Chord Melodies I’m kind of applying these concepts without knowing and always look for notes within the chord and the Major Scale, but also how they sound with or against the chord. This idea of the root, 3rd, 5th…my next exercise will be to play some chord melodies and see what I find…great discoveries to come 
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At first it was difficult for me too, but over time it got easier. Nowadays I can find the general region of a note (within 2-3 frets) relatively quickly. Intervals ear training certainly can help with that.
Spot on Silvia!
I learned about targeting chord tones from an improvisation perspective and then realised that song melody targeted chord tones in the same way. You’ve found it by comparing chords and chord melody.
Although these great discoveries have been made millions of times before us, they are still big discoveries for us and move us forward in our playing and understanding of music.
Have you seen Richard’s @Richard_close2u topic in the “Tips” category about targeting chord tones using a Chet Atkins lesson? Chet Atkins lesson
It’s very good! Richard, as ever, gives a very thorough explanation of how it works and some exercises for you to play around with.
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I can’t say I’m any good at that yet, but I have definitely improved. I came from a place where rhythm was easy but I didn’t even really listen to the melody in a song. Those ear training exercises on finding the tune to happy birthday… er, what was the tune again? I had no sense of melody or melody memory.
What has worked for me so far is a bit of transcribing. I can’t say I’ve done a lot yet. It was super frustrating in the beginning. The other thing that has helped is practicing bends hooked up to a DAW with a tuner, so I can see as well as hear if I’m in tune.
Along the way something starts to click.
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Thanks David @BurnsRhythm for suggesting another lesson in this topic, I will check it soon! 
Joshua @Jamolay it was pretty much the same for me as Jk and from feeling it a heavy struggle, now far from being easy it feels challenging still, but not “mission impossible” as it used to.
Jk it was exactly the other way round for me! My ear was totally caught by the melody only! Weird…I kind of feel that finding the melodies notes on the fretboard started improving together with my progress with Rhythm 
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Shows how unique everyone’s path is, we all have different challenges!
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