The first reference for Atlys is DIGILENT that produce the board and released tutorials to start;
The most important resource for FPGA in the board is obviously Xilinx's references;
There're few pages (that I read) on the web that discover about ATLYS, I will put some link inĀ Bibliography & Reference page.
In this page (updated at 2012.07.11) you can find a piece (required for the guide that I've written) of the references listed above and other files that I've wrote in test-phase of the board.