I've been playing about 6 years, and it is only until these past couple years that i took lessons and learned a good amount of theory.
I've learned my scales, modes, chords(construction, inversions,progressions), and plenty of other helpful techniques and patterns

but i can never really get a full understanding of certain things just from videos and websites and books.

I would like to know more about how rhythm guitar and lead work together.
I play lead

examples- if we are playing in the key of C, the rhythm would play chord progressions in that key. Am i just supposed to play the c major scale? can i use or change to any mode withen the key (e.g. a aeolian, d dorian)? am i suppose to move to different notes or modes along with each chord change?

and what about embellished chords, 7ths, augs, dims, sus, etc...
it would seem if there is some guidelines for triads then there would be more strict guidelines for these embellished ones

its just been annoying to go through books that explain theory, how to play rhythm and play lead, but don't explain how to "harmonize" (if thats the appropriate word) them

Well first step to doing leads over an original rhythm is to find a progression you like. I-IV-V(think twelve bar blues style) is a very common and basic progression. Lets say 2 measures of I, one measure of IV, one measure of I, one measure of V, one measure of IV, one measure of I, then one more of V. In the key of C(we'll be using the Aeolian mode to do this so think in accordance to the degrees of the Aeolian mode), the notes would be 1-A, 2-B, 3-C, 4-D, 5-E, 6-F, 7-G. The notes we'll use are 1,4 and 5 so we'll use A, D, and E. These(depending on what point in the progression you're at) are what i call "Target notes" these notes will be especially effective when soloing over the previously stated progression. Normally, you would want to embellish the solo with other notes in the scale, but these ones are always gonna be safe to land on, as long as you keep track of the progression, and know which one is the "Target Note" at what time. This is the same idea with every progression. There are definitely other good notes to land on, but these ones are never a bad idea.

Key idea: Know progression/Scale to use, know what notes will be effective.

I hope I'm not wrong, as I am UG's Biggest Idiot.

EDIT: Yes you can use different modes of C.
'Synchronising' is all to do with time - I thought that your problem was playing over a backing track.

If you're playing in the key of C, chances you'll have F, G Am, Dm and Em chords as well as C in the backing track - you play notes from the particular chord over the backing track. Analyse the chord structure and note what sort of chords you have to deal with.

Another technique which I use is to write a lead line, put it in Guitar pro and then play random chords until I find a sequence that fits the lead line.
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Holy crap, check this out!
ok, so I can pretty much play whatever I want in the scale but the chord notes are very consanent, so it sounds good if I play those notes.

well that seems simple enough, but one more question about that example
you used I IV and V in the key of c
that's Cmaj, Fmaj, and Gmaj
you chose the notes A, D, E. That's the 1st, 4th, and 5th of the aeolian.
when you say think of accordance in aeolian mode, am I suppose to shift the chords to Amin, Dmin, and Emin?

thanks broham
Quote by Dio10101

EDIT: Yes you can use different modes of C.

All was good until I read this.

When playing in the key of C major, you use the C major scale. You don't use A aeolian or any other mode that you've listed. They all use the notes of the C major scale, and therefore when used in a song which is in the key of C major, are the C major scales.

This issue comes up quite a lot in the MT forum (though I really don't know why).
And no, Guitar Hero will not help. Even on expert. Really.