You can only use a single mod folder at a time, but you can combine different mods into that single folder.
If you are careful about it.
My main mod folder is KHSM (Kryo's Hull System Mod).
Into that I have added elements of the Star Trek mod, some elements of other mods, as well as some of my own.
If there are elements in files of the same name and location, you will have to cut and paste them into a single file.