How do you clean up among your mods?

I use a few different methods.

First I use Curseforge, which allows me to see many of my mods, with icons, so that I can more easily find which to remove. Another method, for those without CF icons, I use sims4studio, where you can see any cc in game and remove it if you don't want it. Both these method work very well on CC, where there is something visually to look at. They also work very well in tandem. 

For mods, rather than CC, CF can also add a visually easy way to see, identify and remove mods based on their names. With these, I do on occasion remove many (most if not all) and start over. To make this easier I have identified a few mods and makers that I just don't want to live without (and that updates fast, preferably through CF), and use a lot of their mods rather than many different mods. I find there is less risk for conflicting mods that way, and they're easier to keep track of for me at least. So on patch day, I usually remove everything, then add mods back one by one as they're cleared, also considering if I really need this mod with my current gameplay. It means patches are a bit of a restart each time. 

I hope either of this can help.