Ok, merges.... Basically, if you follow the guide exactly, you should be able to deactivation the mod where esps that were merged were from otherwise there will be instructions to do some cut and pasting to create new mods for esps that are in those mods that were not merged. If you set up Merge plugin correctly, all assets in the mod will be copied over to the merge mod folder with the merged esp. I recommend you compare the contents of the to be deactivated mods to the merged one to convince yourself that all the content is there. However, even I, who thought that I followed the instructions exactly, didn't keep the patch esps separate from the main mod and when I got to the merge, I realized I had to reinstall the mod and then reinstall the patches separately. When you go through it, you'll see what I mean. So that generally answers your question. Try a couple, and you'll get the hang of it