Is there a way to separate out plug-in options for different functions, but still load the plug-in as one file?

What I'm attempting to do is combine the zenFB plug-ins into one plug-in that's downloaded, but I'd like to maintain separate option groups under the plug-in options.

So right now there are zenFBLike, zenFBComment etc... I'd like to maintain that instead of having one large group of zenFBSuite which is the combo file of all of them.

No sorry but you could "prefix" the text (like "zenFBLike ") so they are ordered by that. You can also set the order manually. Look at the contact_form options on how to order.