@KennaKilla22 I usually keep my mods together and separate from my CC. CC will rarely cause that kind of problem. Since all the files in my mods folder is 95% CC and only 5% mods, I can usually test all the CC at once and it rarely causes the problem. Then I only have to go through a few dozen mods, which doesn't take too long.
Being a bit OCD about organization has saved me a lot of time. Especially since mods tend to break with every update.