No. Install all mods into their own folders (as most mods do by default). Then, open up Path.txt in the folder where SE4 is installed and change it to the path of the mod you want to use (relative to that folder). Set it to "none" to use no mod. Check the readme in FQM for this info (in a little more detail).
Alternatively, look for the SE4 Mod Launcher, which I find to be much better than manually altering Path.txt every time you want to switch mods.