Some of the books mentioned are great reference manuals, if you can read them cover to cover more props to you (i don't have the patience anymore). However, through my college classes I have found that a good math book is better than most programming manuals as long as you understand the basics. When you start, you must first define your variables and terms (what does "x" mean). From there it's simply logical scenarios. If, Then, Else If, And, Or, >,<, =, +, -, etc. From there you have simple commands like PRINT, GOTO, READ, etc. which is what a good book reference is all about.
You also seem to be asking about compatability between programs, or communication. If I'm right (new to arduino), and other members can help me out on this, but I believe you're looking for "Serial Communication" in Arduino. From there you can use "Processing" to collect the information and make it into something useful.
Hopefully I answered your question, and other members should check my post for errors...i'm new to arduino too.
Some of the tutorials that include Processing might be able to answer your question better such as A Touchless 3D Tracking Interface - Make: