In my experience with Circuit City rebates, the CC half states a copy of the UPC barcode, leaving the original UPC for the manufacturer rebate.
As an example, I bought a Netgear PCMCIA NIC at CC yesterday (really!), which has a CC $20 MIR and a Netgear $10 MIR. When you buy the item, you get the regular register receipt, plus two "rebate redemption forms" (printed on the same register paper). On the CC rebate form it says to send itself, a copy of the receipt, and a copy of the UPC barcode. On the Netgear rebate form it says to send itself, a copy of the receipt, and the original UPC barcode. And yes, the rebates go completely different places. In this case the CC rebate goes to Young America, MN and the Netgear one to Phoenix, AZ.
Hope this helps.