Inquisition - possible for too much mods?

Yes, what I want to be sure of is that when I install mods using Mod manager, I have to merge the patch. Then, If I want to change an outfit to another mod, it's disable mod, merge, then put in the new mod, and merge gain.

Is all this merging going to mess up my saves? It's a weird thought, but I have about 10 clothing mods I want to try that all will have to be disabled and merged to work at different points. Most of them just re do the pajamas and formal wear, so loading 2 at once borks up the game Also hair mods that replace the ones in Black emporium, some are replacers for the same hair mesh, so it's back to merging and re merging again. This could happen a lot with modding.

All the merging . . . Just don't want to overdo it.

I've done a little of what you're doing. However, unless I change my mind or forget something I make my patches before I start.

After I decide what other mods I want to use throughout the game I:

1) Choose all the different hairstyles I might want to use during the game. And, to make each pt a little more unique, I change some hairstyles for other races so my dwarf ponytail isn't the same as an elf ponytail or a human ponytail.

2) Decide what outfits I want for beginning, pre-Romance, Black Emporium, Romance, post-Romance, Haven, Skyhold, Trespasser, whatever.

3) I put them all in the mods to merge folder. I have a bunch of sub-folders too so that I can put all my pj mods in the same folder. That way they'll all be listed together when I open Mod Manager for merging.

4) Open the mod manager. By default, all mods are enabled, which means your pj mods are going to overwrite each other. Well, you know this already. I start with the beginning. I disable all the pj mods I don't want to use yet. There's an option in the lower write you can check to customize your output. I don't change the path, but I will add to the new patch name. That is, instead of just PatchModManagerMerge (sorry, going by memory here) I'll call it PatchModManagerMergeKL. In this case KL is for my Inquisitor, Ka'inelle Lavellan.

5) Merge. When finished, DO NOT CLOSE MODMANAGER.

6) Disable your pjs and enable the one you want next, say Haven. Now you need to change your patch name again. Say, PatchModManagerMergeKLHaven. 

7) Repeat steps 5 and 6 until you have all your planned options. Some textures might work in Descent or Jaws but not in BE, and so on. You'll need to make your patches accordingly.

8) When you're done, you might have 10 different patches. Move all but the one you want to use right now to a separate location.

9) Start your game. When you're ready to switch, you just need to close the game, swap out your patches, and reload. 

For me, this is a lot easier than than merging in the middle of the game. I've never had a problem when I changed my mind about something after seeing it in game and needed to exit so I could create a new merge patch. You might guess that I have a lot of mods, at least 1 per hairstyle, 3 different pjs, some furniture mods, a few misc mods, and a lot of crafting related mods. I like to change up the fabric and leather textures per playthrough as well as deciding on a color palette for each Inquisitor, which can mean a lot of separate files as well as planned overwriting (don't need to get into that). 

Hope this helps.
8/9/2017 - Alternately, you can create folders for each scenario. For instance, ...My Games/DA3/Ka'inelle Lavellan/Haven and ...My Games/DA3/Ka'inelle Lavellan/Skyhold and ...My Games/DA3/Ka'inelle Lavellan/Emporium. Then you can use the defaults instead of naming each patch, simply move it to the appropriate folder.