First off sorry if this is in the wrong place, I wasn't entirely sure where to put it..

So basically I want to start playing a new save about with some Japanese cyberpunky style stuff and add a load of custom content, as well as lots that come with cc. My question is am I okay to put all this CC in a seperate folder within the mods folder, and then remove them from my mods folder when I play other saves so I'm not overrun with clutter? Obviously I'd have to put the mods back when I run the cyberpunk game but will it fudge everything up if I load a save without the CC used in it? ie. Will it remove the cc or lead to errors in the other save I'm not playing? Same principal applies to historical games.

Let me know if anyone has a definitive answer on this (or even a vague idea :p)