They're all "run" simultaneously. There's a mod manager program used to install and maintain them. Basically, it inserts data into a folder that the game consults during loading, replacing or adding content according to what's in the folder. I think. I don't know how Bethesda designed it, but the basic gist is that most of their sandbox games are designed with modding in mind. Files in this folder override the content of the base game, or add additional triggers that add new content.
A large number of them are performance enhancers, and many others are changes to systems or rules that I don't like. Those tend to be very small, either replacing wasteful resources (often textures or models) with efficient ones or changing a few lines somewhere in the game. Some are new content, ranging from dozens of new weapons (including models for each) to a new hairstyle because I wanted to see how the physics engine handled hair that used it. A very few, like SkyRe, are gigantic, affecting nearly every aspect of the game and requiring its own utility to handle the generation of compatibility patches for mods that affect the same files.
It sounds like there's a lot, but probably well over 50 are just tweaks or patches that I consider strict upgrades, and will automatically install no matter what I'm doing. They just sort of pile up as you see stuff that makes you think, "This would make the game better".
There are other posters here who get heavier into the new content stuff, although I can't think of any off the top of my head. I've had more myself - these are mostly refinements on existing concepts, since I trimmed a lot of the fat I wasn't using after last time.