So bwarner's answer is almost right.
What it should look like is:
Target: "C:\program files\steam\steamapps\common\sid meier's civilization iv beyond the sword\Beyond the Sword\Civ4BeyondSword.exe" mod=\Fall from Heaven 2
Start in: "c:\program files\steam\steamapps\common\sid meier's civilization iv beyond the sword\Beyond the Sword\Mods"
The way it finds the mod from the directory is by using the
Start in:. This allows you to place your mod in a directory that you feel is more comfortable. For example, if you want to edit your version of
Fall from Heaven 2 because you think the Armageddon counter is good, but should really be about 15% faster; you can make a copy in a different directory and modify appropriately without affecting other users of your computer. Bear in mind, if you load the mod from Civ 4 it'll use the default path.