Skyrim and Boss not recognizing my nexus mods

[Cbode1]

First, I'm not the most experienced when it comes to modding, but I've been able to make everything work most of the time. I used to play skyrim, but decided I was bored of it and deleted my skyrim folder, as most people suggested that that was the best way to entirely erase all saves, mods, and loose skyrim-related files. Lately I decided I wanted to take up skyrim again, and reinstalled it without any hassle. I've been downloading mods from the Steam Workshop without any trouble at all, but absolutely ALL of my nexus mods are absent from the data files and the game itself. I ran BOSS to see if maybe it could make sense of what was wrong, and found that it, too, did not account for any of the nexus mods. As far as I'm aware, all the Nexus mods were downloaded and activated properly, and should be running in-game. Yet none of the Nexus mods seem to actually make it into the game. To reiterate, mods downloaded via the Steam Workshop run perfectly, yet Nexus mods are entirely absent, despite having been downloaded and activated. My best guess is that I somehow screwed up a directory somewhere when I deleted my skyrim folder from (C:\Program Files (x86)\steam\steamapps\common), which is causing the disconnect between NMM and my actual skyrim game. I feel like to someone with more experience, this should be a quick fix. Any ideas?

[saurusmaximus]

If you go into NMM, click on the "Settings" button (the one with the little gears), open it and go to the "Skyrim" tab. Down towards the bottom there is a spot called "Skyrim Directory"; the location given should be the same as where your game is installed. If it isn't, change it so it is.