At the top of the reference theres a link to an extended reference, it has some extra info on less frequently used stuff.
These two should give you a good understanding of the programming.
It's basically just a subset of C (and some C++).
There are standrad C functions you can use that are not in the reference, like sprintf, atoi, itoa.
If you look at some of the AVR microprocessor sites you can find further info.