You can do multiple cgminers pretty easy. Then you can specify the usb spot for each miner. Having 2 would not be to bad to do.
I actually ran 2 on for a while as I had these that have the nice gekko-cgminer, but I had some prototypes and europe one I ran as Icarus.
Yes, just add "--usb :#" to the comand line, on 1 of my Pi-2's, my rc.local file looks similar to this
sleep 8s
cd /cgminer-gekko
sudo ./cgminer -o pool:3333 -u XXXXX --usb :1 --compac-freq 250 --suggest-freq 8 --widescreen --worktime -o pool:3333 -u XXXXXXX
sleep 8s
sudo ./cgminer -o pool:3333 -u XXXXX --usb :4 --compac-freq 250 --suggest-freq 24 --widescreen --worktime -o pool:3333 -u XXXXXXX
sleep 8s
sudo ./cgminer -o pool:3333 -u XXXXX --usb :5 --compac-freq 350 --suggest-freq 50 --widescreen --worktime -o pool:3333 -u XXXXXXX
--usb :1 finds and runs only 1 stick, --usb :4 finds and runs only 4 sticks, and --usb :5 finds and runs only 5 sticks (I don't really need the --usb :5 on the last one, it would just find how ever many sticks that's left not running and use them).
By the way, the "sleep 8s" is just an 8 second pause between booting up and between cgminer starts, just a little extra time to be fully booted and each cgminer to be started. And because it's in the rc.local file, as soon as the Pi boots, it starts mining.