Hi all,
Do you have some suggestions about learning music theory and how to switch from learning scales and arpeggios to apply them.

I can consider online resources or books.
if you want to start at the beginning, i like the complete idiots guide to music theory. it's not guitar-orientated, though, more piano IIRC.
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Tonal Harmony is a very solid theory book. Not sure if this is the most recent edition or not but this is what it looks like http://www.barnesandnoble.com/listing/2671632069055?r=1&kpid=2671632069055&cm_mmc=GooglePLA-_-TextBook_NotInStock_75Up-_-Q000000633-_-2671632069055

The "A Modern Method For Guitar" books by Berklee are really great as well.

Chris Letchford from Scale the Summit has some really solid books out as well.
Troy Stetina's Fretboard Mastery is great and specifically aimed at guitarists.
I make backing tracks for bass and guitar players. Check 'em out here.
Although there is a lot about theory on the internet, it's a very dry way of getting to know it, a bit like learning another language from a book alone.

Better would be to find a teacher that knows their theory inside out, and learn from them with practical application at every stage, examples and feedback.