Hey Tripp. Don't worry as confusing as it all sounds at first it is all surprisingly simple and logical. The best place to start believe it or not is learn your major scale. Yes the major scale....the gayest sounding sequence of notes ever assembled. (I secretly find some uses for it but let's not tell anyone.) The reason you need this is because all of the other modes are derived from this scale.
The major scale has 8 notes from its root to octave.

I II III IV V VI VII octave

In a C maj scale the notes are C D E F G A B

Now if you take the major scale and start on C you have C major. If you start on the second note (II) D you have D Dorian. You use the same notes as the C Maj but when you start and end on the D note it becomes the DOrian mode in the key of D.

The third, E, becomes E Phrygian.
The fourth, F, becomes F Lydian.
Fifth, G, is G Mixolydian.
Sixth, A, is A Aeolian (your natural minor scale)
And seventh, B, becomes B Locrian.

So if you know the major scale in any key you can figure out:
I -Ionian
II -Dorian
III -Phrygian
IV -Lydian
V -Mixolydian
VI -Aeolian
VII -Locrian.

Now after learning that you need to learn how to USE the modes over chord progressions and in melodies. C Phrygian wouldn't sound to great over a progression that is C, G, Am, F.

I suggest at first you memorize your major scale up and down the neck. And how it's intervals correspond with modes. After that the rest will start to seem much simpler.
A good site to check out is http://www.ultimateguitarpage.com
It has enough on there to get you going and of course there is always this forum to ask questions right?