If the mod specifies Twilight of the Arnor (TotA) as a requirement, you can use it right out of the box by simply following the installation instructions of the mod, because the UE automatically starts TotA.
If the mod specifies Dark Avatar (DA) or Dread Lords (DL), you can still use it, but it is a little trickier. First follow the installation instructions. You then have to start the respective game manually, because the UE game launcher doesn't give the option to change the chapter. The necessary files are GalCiv2.exe for DL and GC2DarkAvatar.exe for DA. You should find them in your Steam folder under steamapps\common\Galactic Civilizations II - Ultimate Edition and steamapps\common\Galactic Civilizations II - Ultimate Edition\DarkAvatar respectively.
If a mod doesn't specify for which game version it is, you can use it's release date as a guideline:
2007 DL or DA
2008 DA or TotA
2009+ most likely TotA
As a general rule:
Mods that add pictures or change sound effects/graphics most likely work with all versions.
Mods that modify xml files or other game files work only with the version they are made for.
Hope that helps.