When I load a mod, is that the only one I can load?

Is it possible to just effect the main game itself without having to load a mod.

Or are they specific to what your trying to combine?

When I load a mod, is that the only one I can load?
Yes.

Is it possible to just effect the main game itself without having to load a mod.
Yes, much the same way you'd edit a mod, but it's not recommended. Backup any files you change.

Or are they specific to what your trying to combine?
The exact process is different when combining different mods. If two mods change the same file, you have to include both changes. The easiest thing would probably be to start with one mod and add the desired changes to it rather than try to incorporate two mods into each other.