I have been playing exclusively acoustic ever since I picked up a guitar. I recently bought an electric guitar. Started watching some lessons on YouTube and stumbled across a few related to alternate picking. These videos mentioned that we need to alternate pick every single note. But what I found almost impossible to do is to alternate pick when playing a lead line with an odd number of notes on each string. I inevitably end up using two simultaneous upstrokes or downstrokes when switching strings. I guess I have been doing this ever since I started playing lead on acoustic and didn’t really focus on strictly alternate picking every single note. I always thought it was ok as long as I am alternate picking about 90 percent of them. Any ideas on how to fix this?
What you describe is called economy picking, and that’s a valid technique as well.
Many of the super fast shredders uses it, since (as you’ve found out) it makes it easier to play an uneven number of notes per string efficiently. So, as such, there is nothing that “needs” to be fixed.
The benefits of alternate picking is that it’s a lot easier to be rock solid with timing/rhythm. Another school of technical players have arranged their entire lick catalog around never having an uneven number of notes per string! They simply don’t play those licks (or, get around the problem by applying strategic hammer-on’s and pull-offs).
If you’re new to the idea of strict alternate picking, perhaps seek out exercises that specifically trains this (so - licks or exercises designed to work well with this technique). At least as a start. Don’t confuse practice with playing 
At the end of the day, don’t worry too much about it… just play the lines you want to play with the technique that feels natural to you!
Aah, alternate picking.
My teacher can go nuts when i make a mistake against that. He’s really devoted to this and defends this stance, which i can follow, with what @Kasper said. It gets you rock solid with the rythm.
My thinking about this is: if you’re comfortable with your style of picking, alternate, economy, other, then do just that.
If it works for you, and the songs, wether it’s lead or rythm, you play sound great, then i don’t see an immediate problem.
It’s easy to get influenced by things you see on the net, but remember, if it sounds good, it is good.
If you really want to improve your alternate picking style, i’d recommend you go slow. Start with a very slow tempo, and keep an eye on your picking hand. It’s easy to make mistakes.
Keep in mind that you’re “programming” your body with new information, and that will take time before it becomes second nature.
Here are some excersises i’m using for practice. Never mind the speed part, that comes later. Much later…
My 2 cents.