http://www.at91.com/linux4sam/bin/view/ ... ingStartedI'd recommend buildroot.
You can use gcc to compile applications, either using the same cross-compiler you used to build the Linux image, or on the target if you put the tools onto the file system.
Not at all familiar with Linux, try some books on the topic
http://shop.oreilly.com/product/9780596002220.dohttp://shop.oreilly.com/product/9780596005658.doThere are probably better books out today, but I started with these. Google around for tutorials if that's what works for you.
Dig into the source, and play around, it is open after all.