Merging Mods, it's been too long

[ErrantPursuits]

So, I'll admit this is just me reaching out for some validation on my understanding, or course correction if I'm wrong.

 

I want to install more mods than the load limit of *.esp's allows. I usually try to take advantage of Bash and Merge to reduce these numbers and clean up the process for Vortex. If my reading and user+ level of experience holds true, I should be safe merging mods along these rough groups:
Clothing/Armor (Outfits)

Animations

Textures (Appearances)

And then I can fold that into Bash and Proc patchers as required. This may include 50 or more small mods merged at a time.

 

Second line of inquiry:

Last time I went through this process some mods had masters that were made obsolete by ultimate edition. Is it safe to edit the required Masters, do I need to check all the references through Creation Kit? Is there a good tutorial or reference document for the process? I just feel like my information on how to resolve some of this has become really out of date and I'm struggling a bit here.