Then I noticed in the sticky here about compatibility:
- Wrye Bash: That's the most important tool. It's essential - if you use more than ~25 mods chances are good that you already have an incompatibility issue solveable with Wrye Bash. Main component is Wrye Bash's Bashed Patch. It can integrate several mods changing the same record (see rule of one), so that all changes are there in game. Example given: OOO and Spell Tomes do both change the same leveled list. Without Wrye Bash only the last loaded one will win and overwrite the other, but by simply using Wrye Bash's bashed patch both will work.
That....sounds....awesome.
So. How do I get started learning this wonder tool?!
I found this: http://www.uesp.net/wiki/Tes4Mod:Wrye_Bash/Bashed_Patch but even that assumes somebody knows what they are doing with Wrye. I need to go a few steps before that since I can't understand half of that article.