One thing I'm sure of is that it DID give me a prompt asking whether or not I would like to use NXM links, and I'm pretty sure (about 90%) that I hit yes. At the time, I was following a guide but it must have been outdated because the instructions didn't match up with my own experience. It seemed to differ a little bit from MO in that it did not install to the folder I made for it in my SSE directory, nor did it ask where I wanted it to go. I believe this is user error and not necessarily a failure to function properly on MO2's part. It appears as though MO2 will not download mods from the Nexus via 'Mod Manager Download' button.