I just make desktop shortcuts for different mods.
"D:\Games\SteamGames\steamapps\common\7 Days To Die a21\7DaysToDie.exe" -UserDataFolder=E:\SaveGames\DF
That is my shortcut for Darkness Falls.
If I were to do Undead Legacy, it would go...
"D:\Games\SteamGames\steamapps\common\7 Days To Die a21\7DaysToDie.exe" -UserDataFolder=E:\SaveGames\UL
And for every set of mods, I just use a custom save path. I also do this to the Vanilla game so that my saves go onto a different SSD than my OS.