You won't technically need to reinstall it again. In the directory that z-bee's mod manager gets installed (C:\Program Files (x86)\zBee14 on my machine) will be a file called "z-Bee 1.4 CMSF Mod Manager.accdr". The mod manager is just a microsoft access database, so if you make a copy of this file you can set the second copy up for CMBN, each file is a completely separate database(making each file a completely separate mod manager). This can be done as many times as you want, one for each CM game. I just renamed the copies to what game I was going to use that file for then setup an icon for it.
Edit- forgot to add that the copy will have the settings saved from the original file as well as the mods installed. The directories you will need to change first, then for the mods you can deactivate them each, then remove them from the mod list. Without changing the directories first you'll deactivate the mods in CMSF, if you change the directories first then deactivate a mod it'll say that the mod wasn't found in the z folder(this is what we want to see)
advanced computer user - you can open z-Bee14CMSFModManager.msi (the install file for the mod manager) using 7-zip and it'll have the original database file, which can then be extracted where you want