As I wanted to share my experience with the Alix 2D13 hardware I got last year, I split up my notes in some more or less logic parts.
I wanted to attach the antennas on the back, so I had to drill 2 holes.
As I missed a proper 6.5mm drill, I drilled two 6mm holes and used a rasp until the antenna plugs fitted in. The holes are located 5mm from the upper and the side. If both antennas are attached, you can not attach the serial cable, but thats not a problem to me.
There are some pictures and notes on attaching a hard disk to the alix 2d13 here.
After covering basic debian installation, we configure networking, this includes claiming a /48 tunnelbroker.net IPv6 addresses, so we can provide IPv6 via wifi, and basic firewalling, afterwards we configure dns&dhcp.
Last but not least, some bits how to use the hardware encryption, the embedded AMD Geode LX Security Block Device via AF_ALG on kernels >= 2.6.38 in userspace via openssl. Contrary to CryptoDev, which never made it into the mainline, AF_ALG does not require patching the kernel.