It took a little searching to figure out how to setup two UPSs on one Nut server. The trick is leaving the port set to auto and using the serial number to differentiate between the two UPSs. Running lsusb -v will output the serial number of the usb devices you have attached. Now just add the second UPS to the ups.conf and set the serial number for both.
maxretry = 3
[apc-1500]
driver = usbhid-ups
port = auto
serial = 3B1XXXXXXX63
[apc2-1500]
driver = usbhid-ups
port = auto
serial = 3B2XXXXXXX28