Along with learning the modes and scales of the guitar, I have found it important to also learn intervals.
In this excellent lesson from David Wallimann, you will learn intervals. It includes an excellent description, along with diagrams for us beginners.
Get the full Applied theory pack at http://www.guitarplayback.com/theory
This package will explain to you in depth everything you need to know about modes, intervals, scales and applied theory for the guitar.
This extensive video course should answer all your questions on the subject.
All videos are in .mov format compatible with PC and Mac
All diagrams and backing tracks included