RE: Number of mods
I'd suggest you should create a separate mod (as a separate mod folder) of each of them you might want to use. Then, just activate them one by one using JSGME.
JSGME will give a warning if the next mod activated should replace one or more same files Than what a previous one did. Should that happen you can consider what that means. Or simply try out. It is easy to roll back a mod with JSGME so there is no risk trying.
I would recommend against combining mods into one folder unless you truly know what you're doing per mod. When you do know, that is an option of course as well.
Hope this helps. As said, very easy to try out with JSGME as anything put in can as easily be taken off as well!