Honestly... While merging files with S3PE is great, S3PE is touchy. It doesn't like a lot of files at once, which reduces how much you can merge together.
If you go to MTS and get The Custom Launcher - It does this all for you, and it will merge everything together for you into a few simple files. I have around 1,000 CC / Mod package files in 4 package files now because of the Custom Launcher, and I have no issues what so ever.
Another advantage The Custom Launcher has over hand doing it w/ S3PE is that you can merge Mod Files (not just CC like hair/clothes) because it lists everything, by name in the user interface of the launcher. Allowing you to remove the mods when you have to update them. If you merge mods w/ S3PE you can't separate them later when they need updating. D=
