Welcome dwatt.
There is no way to separate the recordings the way you suggest. Technically, you don't have 2 PVRs. You have 1 PVR with a hard drive that stores all the recordings and one set-top-box that is able to control the PVR to set up and watch recordings.
The only programs that are put in folders are series. If you set up a series recording, all the new recordings for each series will be put in a folder and cut down on the number of programs you have to sift through. If you record the individual programs they will all show up in the main list.