Unfortunately, this information can be difficult to read for non-engineers (and even for engineers too!). Usually this information is only useful for performing direct access to the timers, uart and other on-chip peripherals, when existing example code does not give exactly the results you need.

Atmel's Official Page

The Official Atmel Page provides this datasheet and other information. However, most of their code is NOT compatible with GCC (it only works with expensive commercial compilers).

Atmel uses a different bootloader called "DFU", which is different from HalfKay on the Teensy. DFU takes 4K of the 16K flash memory, whereas HalfKay uses only 0.5K! Atmel's FLIP tool only works with DFU. You need to use the Teensy Loader with Teensy boards that have HalfKay.