Lord Drake
Paper Tiger
There are just two ways basically, and they both end up achieving the same. A mod should be a single subidr underneath <Civ4>\<BtS>\Mods, how you get that done does not matter.
If the mod is an archive (.zip, .rar, etc.), check if it contains a single directory, if it does, extract it to <Civ4>\<BtS>\Mods, otherwise (i.e. if it contains files and an Assets dir directly), create a dir in that directory first and then extract to that.
If it is an installer, point to that directory (<Civ4>\<BtS>\Mods) and install. If it still manages to end up being in the wrong dir, just move it there.
You have to be careful about what mod and what version of CIV you use though, there are some mods for Warlords rather than BtS and some mods for older versions of BtS which have not been updated yet.
As long as you stick to mods for BtS 3.19 (assuming you use the latest patch), you are fine with the above.
huh.. that's the most clear cut explanation i've seen. :/