More information can be found in Robin’s 0.60 FAQ post. Please be aware of the risks in doing this. If you are still using earlier versions of NMM (before 0.60) then there will be a transition period while NMM uninstalls and reinstalls all your files for other games (like Skyrim). Profiling is very effective at making mod management easier and more convenient (with sharing functionality coming soon), but also drastically changes how NMM handles file storage and mod installation behind the scenes.
Please know that this release also includes the “Profiling” functionality added in recent releases. Even fancy scripted installers should work, though we haven’t had a chance to test them thoroughly yet as there's no mods that use scripted installers out at this time. This is a preliminary release that may have some wrinkles to iron out, but internal testing has gone smoothly. It’s been amazing to see the reaction to Fallout 4 modding so soon! We knew it was going to be big, but the response has been phenomenal! So, DuskDweller and Luco81 our illustrious NMM dev team, have been working like Dogmeat updating Nexus Mod Manager to handle Fallout 4 mods.