The Faerun Map remains in the "map" folder, where I assume you have it installed if it is working correctly.
Better Independants is a mod and goes into the "mods" folder. You can use it with Faerun (or any map). To use any mod you go to Preferences->Mod Preferences->[click on mods to enable them]. Then start a new game. Any mods enabled at the time of game creation will be incorporated into that game. If you load any previous (saved) game Dominions recognizes the mods you started it with and automatically loads those mods for you.
In general all maps are compatible. However, mods rely on a limited set of Identification numbers (for units and such), so if two mods use the same Id numbers for different stuff then weird results can happen (from getting the wrong unit/spell/armor/whatever to the game crashing). It is an easy fix though, if you just look into a little modding. I thing Gregstorm (or someone?) made a nice mod-reconciler tool that fixes such errors.
Some maps (like the Dom 3k maps and the Antilarium map) require certain mods to work properly, but beyond that all maps should work with all mods.
Finally, if you enjoy Faerun (which is a great adventure map) you might want to look into Antilarium (
Here) and Gang Wars (
Here).
There are probably more, but those two spring to mind.