MagikPups

I'm pretty new to Skyrim Modding (Just signed up to this like 10 minutes ago!). I've used the SSE mod loader but I don't know how well it will interact with NMM and I'm a bit scared to just upload everything and try it. I'm just curious on if I can use both the in game mod loader and the NMM or if I have to download all the mods from the in game one onto the NMM and purge them from my game for now. Sorry if this is the incorrect place for this.