First download the patcher from the resources section, then run xdPatcher.exe and fill it out as follows, replacing "Patcher directory" with the path to the main patcher folder and "Steam directory" with the path to your Steam installation.

You will need to patch the game a second time to get to the correct patch for any% runs, replacing the top box with the 1.0.6 to 1.0.3 patch, the second with the game installation created in the previous patch, and the third box with any other directory. You will now have three patches of the game, the third one being the one that is used in the any% runs.