Yes, you can use a standalone PVR with either Dish or Directv. I use my Replay 5040 with my Hughes E86 box.
If you are looking at getting Dish, you might also look into getting their new 522 PVR. It will serve two rooms from just the one box, you can watch a different show in each room at the same time, you can record on two different channels at the same time, and you can watch recorded shows in either room.
The standalones work fine with satellite, but the integrated satellite models work much better, with "perfect" video quality, digital audio, & dual recording in some cases. I would sell the standalone if switching from cable to sat.