Hi Justyn-
There are of course many ways to work with the PRU, but if you want "latest and greatest" that would be via RemoteProc framework. And if you are working with the TI labs, you have already been exposed to it.
I don't work with CCS (might in the future as I saw recently there is no longer a license fee), but instead I did everything at the command line via SSH.
And I used the Beaglebone Green with Debian based IOT image (TI kernel). If you look at this project, there is a link to a github repository which has a PDF file in the doc folder.
There are a couple of sections in the PDF which show how to configure it all on the BBG Debian IOT:
RemoteProc framework does the work of loading the PRU firmwares into the PRUs and starting the processors.
It's just an example, have a look and it might give you an idea where to go next.
Regards,
Greg