I also use Wrye Smash for Skyrim.
Which is odd because I could never figure out that program for Oblivion. But in Skyrim I began using it right from the get-go. Why? I'm not even sure. I think Turija suggested it to me back in 2015-2016 over and over.
Just open the Installers tab, drag the archive over, choose which .esps or other features you want, and toggle them on in the Mods tab. I don't know if SE works this way as well (I have the original version). The program just seems way easier than it did for OB. Whenever I'd try to use WB for Oblivion, I'd get all these
red lines all over the page. My game would CTD on launch after opening the program, and so on.
From what I understand, uninstalling mods in Skyrim is a pain, because other some other programs won't uninstall the entire mod (such as scripts). But Bash / Smash definitely does this. I've made sure to have a look into my Scripts folder especially (VERY important) before and after Uninstallation. Wrye always removes them automatically.