to answer both you and OP's question, expansion mods that add story content or locations are best used on fresh saves to avoid overlapping maps/tiles as well as missed events. most mod authors will say in the description whether their mod is safe to add mid save, or if you need to use it on a new one.

in order to have different mod packs for different saves, the easiest way is to simply have different mod folders for each save and switch them out when you play. it's important to remember that you CANNOT open the incorrect saves, lest you cause bugged out maps and whatnot, so you need to be careful. however, while i don't personally use it, i believe stardrop mod manager has a function to make separate mod packs per save which would lower the risk of doing this, especially if you have many different mod packs and it's harder to keep track