I use to use my system with Bell Express vue in Canada. I think they used toi use the same hardware as dish did. I was controlling 2 Bell receivers with a single USB-UIRT. Most of this hardware allows you to assign an address to your remote and receiver. Usually 1 to 15. This way, a "1" command for receiver 5 is ignored on receiver 6 for example. So in a sence, you're setting both receiver boxes up with different IR command sets. Your Dish manual should tell you how to change the address of the STB.
WIN 7
1 X PVR 250
1 X PVR 500
1 X HD-PVR
2 X MVP
2 X PCH A100