Yes. Most rigs you get from other sources will already be assigned to morphs for whatever character you're using as a rig base. This is one of the reasons why I just started making my own rigs from scratch.   You may want to take a moment and just look at the bones Kate came with, see how they're setup and named.  Eye bones are usually connected to the head object or to a dummy bone which is connected to the head.  Make sure your objects have names and seperate material zones before exporting from your modeler. This would normally keep the objects seperate when looking at the grouping in other programs. I have never used C4D, so there may be some dialog box options to check as you export.

Edit: looks like Xantor confirmed my suspicions about the export from C4D. Thanks!