Erm...I really know NOTHING about musical theory, could someone explain to me when to use each different mode?
I mean, over which chords etc..

seven notes in a major scale=seven chords, built by taking every other note:
in c major
CDEFGAB is the scale
CEG is your first chord, it's c major
DFA is the second, it's D minor
etc...
You use each scale on the chord that's built on it...
Or you can use another scale, depending on the sound you want to get in your improvisation.
Think in modes in terms of "sets of intervals" when you change your mode, the intervals between your notes change...
So, playing the major scale, and making the forth one half step higher makes you play a lydian scale...

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So...wait (I'm sorry, I really am a musical dunce)
You play the notes of the scale from which the chord is derived, but if the chord can come from different scales, can you use either?
And do you just play the notes of the chord, or the whole scale?
(Sorry again )

yes, it depends on the context of the song, and of the progression...
as for the notes, or the entire scale, it depends on what type of sound you are looking for... but you can do both

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Ok, and once again, how do I know which Modes work over which scales/chords?

the chords built off the 1st and 4th degrees of the major scale are Major. So therefor the modes built starting on these scale degrees will also be Major. (ionian & lydian)

The chords built off the 2nd 3rd & 6th scale degrees are minor, so therefor these modes will also be minor in flavor (dorian, phrygian, & aoelian)

the 5 chord is dominant, so Mixolydian will also be Dom.

The 7th chord is a minor 7b5, so the mode built on the 7th degree (locrian) will also outline this sound.

so lets suppose your soloing off a D-7 vamp, the most common choice here would be to you's a dorian scale, but you could also use phrygian and aoelian for added color.

This is quite confusing stuff, it takes a lot of trial and error to understand, so be patient, and feel free to ask a lot of questions. The more explicit you can be with your questions the better we can help you out.
Ex; Why does xxx scale sound funny when played over xxx chord?

Thanks, you've been really helpful...
Nice to be able to ask someone