Questions about mod manager

[Szivan]

Hi everyone. Recently I managed to trash my skyrim and had to make a clean installation. I looked up some safer methods to mod my skyrim as to avoid another clean install in the near future, and I want to ask if anyone knows, if you can use the mod manager (the one that does not directly install mods into the data folder) along side the one from nexus, or any tips on how to set that one up, since it even allows you to create separate profiles for individual characters. Since I haven't done much modding without the NMM I would greatly appreciate any helpful advice.