What's the best way to mod Skyrim Special Edition and Fallout 4 using the in game mods?

I would use the Nexus mods but the NMM doesn't work for me anymore (despite uninstalling and reinstalling it) so I have to download mods via the in game menu which disables achievements but what is the point in having a mod system if your character will can't get achievements? I'm not an achievement hunter but I enjoy getting them through playing the game naturally. Bethesda have made mods easier than ever to get but they also added a huge incentive to not use them.
Would it be best to have a mod specific profile or just leave mods all together? I really like my current character.