As of two months ago I was using a combination of NMM, BAIN, and a NMM to bain utility thing. Is there any new and easier ways to manage mod installations?

Nmm, boss and wyre bash is what I use. Nmm for installation, boss for load order, wyre for merging. No problems.

Also, point nmm to bash installers folder (usually end in \Steam\steamapps\common\Skyrim Mods\Bash Installers). This way it marks for you you the updates for the mods installed.