Most mods are simple and it's just a matter of putting the right files in the right place. Since it's beta-quality software and you've probably just run into a bug, I'd advise learning how to cut out the middleware and install mods manually. In the meantime, it might help to know that a mod manager is optional-you can install mods without ever touching Nexus Mod Manager.
If there are installation problems, they'll want to know about it and it's more likely to be fixed there than by asking here. If you're experiencing problems with it, consider reporting the problem so that the coders and other users on the official beta feedback forum can read about it and any bugs can be fixed.
First things first before I get to the advice: Nexus Mod Manager is beta software.
