I keep my chords, above or below where i am writing my leads. And i make sure that they are different tonal characteristics.
To write leads to the chord progression means that you have to have a clear understanding of what you're playing.
to think to much, is a failure in emotion, to not think enough is a failure in understanding.
You also could be restraining yourself a little to much to the chord progression. Often times, i try to think of things as singular parts when writing it out.
If i go back and listen to it over and over again, i may or may not find something that i'll need to tweak or take out.
What you're dealing with here, is a mix of producer/writing difficulties.
I had to compartmentalize those two schools of thoughts after i was done writing the music. It wasn't until i started messing with arrangement that i realize things would be kept or changed.
This is the best i can do to explain it from a less technical point of view, outside of practice, study, and apply that's my advice really.
I'd also suggest you go and listen to classical music, and maybe even try to make a loop or a song that sounds similar that you can jam out to. It might help you understand what you're missing.