I am scrolling through this list: http://www.mwmythicmods.com/telesphoros.htm and a large number of these are catching my eye. Since I have played vanilla Morrowind for years, I feel like modding the ever living ashpit out of it (but still retain the same unique feel the game has). I don't want to screw anything up, though. How do I know what I can or can't use?

You can use anything you want.
MSGO is basically just visual enhancements, so you can add all the content you want with no problems.

Avoid mods that are just different versions of what the MSGO already does.
For example, you don't need a mod that replaces the old trees with new ones, or a mod that has new textures for the armor... MSGO has all that stuff for you. **

New quests, Races, weapons, armor, dungeons, etc, etc.... all that stuff works with MSGO because they don't overlap in content.

If the MSGO is the only mods you installed yet, you'll have to learn how to install mods the normal/manual way.
Info can be found in the Pinned threads. And be sure to get Wrye Mash.


**
(Unless, for example, you hate the new armor textures and want to use something different than what the MSGO has to offer, then you can do that. Installing other armor textures replacers will just overwrite the MSGO files.
Simply running MSGO Options again will overwrite the other mod files and add the MSGO armor textures back into your game.)