#1
what are some good exercises for driving theory into my brain and memorizing the names of the notes on the fretboard?
#2
Using it.

Theory isn't really about exercises, it's not exactly something you can drill - it's simply about understanding what you're doing.
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#3
That's nonsense! There are thousands of exercises that can be done for theory. Get a transcription of a piece you enjoy and analyse the notes in, see what chords are put where and to what effect, what scales/lciks are used over chords etc. For just basic theory drills there's always http://www.musictheory.net/
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