The BEST way is to study with a qualified instructor; you will progress light years faster than trying to do it on your own.
The best way to learn theory is first to learn the C Major Scale, and how it relates to all 8 scale positions on the guitar (These are the 8 patterns you can play on guitar which have different fingerings but the identical notes). Also start sight reading violin studies -- Start with Wolfhart's 60 Etudes for violin.
After the major scale and once you start sight reading every day, you need to learn about scale mechanics and intervals. Ear training then comes into the picture.
From there you learn chord theory, the minor scales, and finally modes. That will put you solidly in the intermediate level of musical theory knowledge.
As far as I know there is not a single book that can break it all down to you, as teachers, methods, and students all vary.
I like the book Guitar Lore by Dennis Sandole; however, it's more of a supplement than a replacement to studying with a good teacher.
Regardless, you will need a LOT of patience and expect it to take a couple of years, minimum, until you get it all down.
Good luck!