I know this question was from last year, but since I just went through it myself, I thought I'd give ya a reply. You've probably figured it out by now, but this thread pops up when people search for Warlock Mod installation on 64 bit Windows. Maybe this reply will be helpful to someone out there.
This is what I did on 64 bit Windows 7. My copy of AoW is from GoG.
1. I did a clean install of AoW, but not in Program Files (x86). That folder caused all sorts of permission problems for the mod. I installed AoW in C:\Apps\Age of Wonders. Anything like this should work.
2. I downloaded the mod, unzipped the folder, and copied it to the Age of Wonders folder. So it was located in C:\Apps\Age of Wonders\Warlock's Rule Set.
3. Within the Warlock's Rule Set folder, I ran the WR136110 program. This will unzip the mod files. Be sure that the path is correct; the default path that it suggests might not be where your game is installed. I had to point it to C:\Apps\Age of Wonders.
4. After the program has unzipped the mod, apply the 64 bit Windows fix files. Download them, unzip them, and copy the three files (CSumWar, Pa3, and Pa4) to C:\Apps\Age of Wonders\Release\Warlock\Pat (or wherever your game is installed). You will already have files called CSumWar, Pa3, and Pa4 in there. Replace them with these 64 bit fixed ones.
5. In the main Age of Wonders folder, run Rules2.bat. The fixed 64 bit files should now make this possible.
6. Finally, download RuleChanger1.5. Unzip it and move RuleChanger1.5.bat into the main Age of Wonders folder. Whenever you want to switch back and forth between normal AoW and Warlock, run the RuleChanger.
Edited to add: When I run the game through AoW.exe (in the Age of Wonders folder), the game shows a special background indicating that the mod is active. However, if I use the shortcut in the Start Menu games - or the link in the Games Explorer folder - this background does not appear even when the mod is active. Just a heads-up![This message has been edited by Loknar (edited 07-19-2014 @ 06:03 PM).]