Yes, in programming the receivers for RF mode, you enter the last 6 digits of the unique RID #, so even if you wanted to control both at the same time it can't be done, so no worries.
Cover one receiver as you program the other. with the receiver and remote in IR mode:
1. menu> settings & help> settings> remote control> IR/RF Setup>
2. you will see either IR or RF, click whichever to reveal both
3. choosing RF, or RF and then Done, the remote will stop controlling the receiver
Do the following on the RF remote:
a. press and hold MUTE & SELECT, wait for two blinks, release
b. enter 9 6 1
c. press CH UP
d. enter the last 6 digits of the Receiver ID #(RID), found on a sticker in the access card compartment
e. press SELECT
repeat for the other receiver, except use a different 6 digit RID # in step d.