Just to add a long time players feel into this...
All the scales and leads etc, that you learn are stuff that is meant to be kept in the back of your mind as you're playing your own material.
For instance, when I'm playing or writing a lead, I'm not thinking about scales at all. I'm thinking of the melody and how I can emotionally effect the listener throughout the solo or the entire song. While I'm doing this, I'm using many years of scales and so forth to be able to construct a solo or guitar part.

I guess the short version here is, learn a whole bunch of scales, solos and songs. Then use your years of experience to play well constructed melodies and leads.