It renders in After Effects. If you don't want to have to render it over and over each time you make a change in AE, you can prerender it like you would with any other render-heavy asset in AE.
What he said. The purpose of the plug-in is to bring the renders inside AE to speed up simple workflows. If you have complex projects that are very render heavy the C4D LTE is not what you need. You need the full version and you should be rendering your passes to image sequences in that case, not to compressed files.
So I figured out my own problem. For anyone else who might happen upon this thread, hope this helps.
At the lab they must have C4D Full (or whatever the full version is called), and at home thru CC I only have Lite. That's why there's no render queue and no ability to set a filename or filetype within C4D.
The workflow I had to do is import the C4D file into an After Effects comp, and then the Cineware rendering options show up in the effects window. Last word of advice is if you need to render out an object buffer to be used as an alpha mask, make sure you select "Standard (Final)" or "Standard (Draft)" under the Renderer dropdown.