I'll presume you are using oscam to read the cards.
Attach your omnikeys then run one or both of the following commands:
sudo lsusb - shows attached devices
opensc-tool -l - shows omnikeys
This will show which usb the omnikeys are assigned to.
Then in oscam.server file you will need two readers. Look at the example below:
[reader]
label = SETANTA
protocol = pcsc
device = 1
blockemm-u = 0
blockemm-s = 0
blockemm-g = 1
blockemm-unknown = 1
emmcache = 1,3,2
group = 1
caid = 0963
services = Setanta
#ident = 0963:000000
[reader]
label = CYFRA
protocol = pcsc
device = 0
mhz = 357
cardmhz = 357
emmcache = 1,3,2
group = 2
caid = 0100
You can see from above that each reader has a different device. By running the commands from above you will already know which device your omnikeys are assigned.
Hope this hasn't confused you more!