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