You can do it as given in 3.7.1 QuickStart Guide, item 9.2
You can use sudo piaware-config [argument] [value]
for original instance of piaware, but this wont work for the second instance of piaware.
For making first (original) instance of piaware to be “1090 only”, follow commands in item 9.2 of QuickStart Guide.
For making 2nd instance of piaware to be “978 only”, you will have to do following:
sudo nano /etc/piaware2.conf
Then add lines (or edit if already existing)
uat-receiver-type sdr
receiver-type none
Save file, (Ctrl+o) and close (Ctrl+x).
Restart 2nd instance
sudo systemctl restart piaware2
Item 9 of QuickStart Guide