I load the game through steam, using the Original Release beta. I then load the mod through the Civ 4 menu.
D:\Steam\steamapps\common\Sid Meier's Civilization IV Beyond the Sword
As for options, I start a custom game, and normally select all victories besides time and quick victories. I change which playing options I pick, but typically I stick with Permanent Alliances, Blessings of Amathaon, and Wild Mana. I'm a fan of the idea of flexible difficulty, but I'm not sure it works right, as I only ever see my difficulty rise, even when I'm in the bottom 3. So I don't pick it every time. Just tried it again, same thing happened. Updated to latested revision (300), no change. Also, sometimes I have issues where terrain features don't even pop up.
I've basically had to take a break from playing, since it's fairly unplayable as of right now. Hoping that it will be able to be fixed though.