Originally Posted by: emusic45I have recently started trying to apply music theory to my playing and I am having a hard time with it.[/quote]
You might find my tutorials on music theory helpful:

Music Theory
http://www.guitartricks.com/tutorial.php?input=495

Circle Of Fifths
http://www.guitartricks.com/tutorial.php?input=835

Originally Posted by: emusic45The problem I am having trouble with is getting comfortable with how to play scales and find the notes in a key without having to think about it.

The only way you will get to the level of doing it automatically (without having to think about it) is a lot of repetition.

Start with a scale pattern, say the major scale. Play it in C major. Say the notes as you play it. Repeat it a lot. And I mean incorporate it in your daily practice. Don't just play it 20 times one day and expect you are done. Play it & say it every day for weeks or months.

Then move the same pattern up to G major, say the notes. This way you will be using the same fretboard shape and the same essential sound (the major scale) but altering the root note, helps you add just one more element, the notes of each major scale in turn. Repeat a lot in your practice schedule.

Make sense?
[QUOTE=emusic45]I tried memorizing all of the notes on the guitar and memorizing scales and I guess it just seems like there should be a better way. Like the scale from c to d is the same but up a whole step. would that apply to all scales?

Yes, that applies to all scale.

Each scale has it's own unique formula (set of intevals in between the scale degrees). Every major scale is:

1 (WS) 2 (WS) 3 (HS) 4 (WS) 5 (WS) 6 (WS) 7 (HS) 1

This is by far the easiest way to understand the major scale. Use this idea to play major scales all over the fretboard. While you are learning to physically play them just focus on that one task. Once you've got some skill built on this task, then start to gradually focus on learning the notes in each scale.

Take your time! Be patient. You don't have to learn it all at once. Do it slowly, systemically & patiently. :)

The notes in all the major scales are in the Circle of Fifths tutorial listed above. Hope this helps. Sounds like Bobby is willing to help you out in real time. That is awesome for you! Bobby is a great player & teacher. Have fun with it!