The safest way to do this is one SDR at a time plugged into the Raspberry Pi. So first, only plug in the radio to be set for 978.
Power up the Raspberry Pi and then SSH into Stratux and do:
pi@raspberrypi ~ $ sudo su -
root@raspberrypi:~# service stratux stop
[ ok ] Stopping Stratux ADS-B Receiver: stratux.
root@raspberrypi:~# rtl_eeprom -d 0 -s stx:978:0
Power the Raspberry Pi down and disconnect the 978 SDR. At this point, you should use a permanent marker and mark 978 on the USB plug housing as close to the circuit board as you can.
Label the second 1090 SDR on the USB housing and then plug it in. Power up and SSH into the Raspberry Pi and do the following:
pi@raspberrypi ~ $ sudo su -
root@raspberrypi:~# service stratux stop
[ ok ] Stopping Stratux ADS-B Receiver: stratux.
root@raspberrypi:~# rtl_eeprom -d 0 -s stx:1090:0
Now, power down the Raspberry Pi and plug both SDRs in. At this point, the correct frequency will be assigned to the appropriate radio.