It would depend upon the mod. Certain changes require the use of altered existing game files. Where you to use two or more mods with the same file altered then you would encounter issues. The vast majority of mods will however work together. With steam workshop I'm certain you will not encounter any issues. 

You dont select different mods, if you have more than one mod installed in the game folder they need to play nice together or you are going to have issues.

Leader FGs, BGs, portraits and logos all need to go into their relative folders in \MyDocuments\My Games\GalCiv3\Factions

Frankly SD needed to take a lesson from either Endless space or their own game Sins of a solar empire for the mod interface.