I downloaded a couple of mods from this site. My Nexus Mod Manager picked them up and shows them in the plug-in's section of the Mod Manager. I checked the boxes and started the game through Steam. I clicked on the data button and ther is no sign of them, and they are not in the game as far as I can tell. I have not went to the location on the map to see......well because they are not listed on my map. I don't know where to look. The mods I am talking about is the one with the pool and maybe some caverns. And the tower of somekind or another. Any way too make a short question long, How do I start plugins? are they automatic or is there somthing I need to do?

At the risk of sounding sarcastic, which I'm REALLY not being, I have to say, DON'T USE NMM TO INSTALL YOUR MODS.

I use NMM to download mods... or did for a while until even THAT was too much of a problem. NMM is very, very, VERY buggy, even for a "beta," bug fixes are not timely or even forthcoming in many cases, updates are very slow to occur and often create more problems than they solve. NMM is, largely, dangerous to use in its current state. It does what it does in very unhappy, unhealthy ways, reporting all sorts of confusing, incorrect data to the user, and mostly leading to problems for everyone that chooses to use it.

I do like the way I can easily see what mods I have downloaded that have since received an update. That's very convenient. Aside from that, NMM is of negative value to me. I want to say more nice things about it, but there just isn't anything to say.

So with that said, I highly recommend that you use Wrye Bash for installing mods. Additionally, if you want to use NMM to download your mods, I recommend that you set the downloads folder to be the SAME as the bash installers folder (used by wrye bash to find installation packages). This will save you a lot of time and hassle.

Once you've downloaded a mod, you DO have to install it (a separate process, possibly as simple as just dumping files in the data folder, or possibly much more complicated than that) AND you also have to activate it. You can do this directly in wrye, or you can use the data files option on the skyrim launcher tab, but there are arguments for using things like wrye or something else to load and order your mods, once they have been installed.

Lots of people have success (presumably) using NMM so YMMV from what I've stated here. But you can't go wrong with Wrye, IMO.