If you say you have the notes of the fretboard down, I'd say the next step is learning about intervals, which are the basis of scale and chord construction (as ZakJenkins touched upon). With that understood, you can grasp the concept of modes much better (I didn't really get it at first either, despite several explanations).

Originally Posted by: BrokenJerathe chords behind the modes is what i call them because i dont know a better name. these are the chords that 'sound' with a mode.

This is often called the "chord scale", as that's exactly what it is...taking each of the individual notes of any scale and stacking 3rds on top of them to make chords that correspond to each interval step of the scale. It is actually very handy for making up chord progressions, or changing keys of known progressions.

Here's a few sites I recommend:
zentao.com - my favorite because it's guitar oriented and well explained on many essential topics with examples, suggested practice, and actual applications.
teoria.com - comprehensive site with articles, interactive exercises, and tutorials.
musictheory.net - another comprehensive interactive site.
cyberfret.com - again guitar oriented, but actually I can't say I've used it much, but take from it what you will.