Sorry I forgot to reply to this. I am running exactly that combination of hardware but use 1 instance of bfgminer for the BE's and the custom cgminer build for the U1's. for the cgminer instance I specify the USB ports using the --usb switch (e.g. --usb 1:23,1:25,1:26 for the 3 I use). To find the usb ports I ran lsusb from a command line with just the BE's plugged in and then ran it again with the U1's in as well. Comparing the difference showed me the ports (below is my lsusb output from all the devices so you can see how to find the port details - the 1 is from the Bus and the 23, 25 & 26 from the Device)
Bus 001 Device 021: ID 10c4:ea60 Cygnal Integrated Products, Inc. CP210x UART Bridge / myAVR mySmartUSB light
Bus 001 Device 022: ID 10c4:ea60 Cygnal Integrated Products, Inc. CP210x UART Bridge / myAVR mySmartUSB light
Bus 001 Device 023: ID 10c4:ea60 Cygnal Integrated Products, Inc. CP210x UART Bridge / myAVR mySmartUSB light
Bus 001 Device 025: ID 10c4:ea60 Cygnal Integrated Products, Inc. CP210x UART Bridge / myAVR mySmartUSB light
Bus 001 Device 020: ID 1a40:0201 Terminus Technology Inc. FE 2.1 7-port Hub
Bus 001 Device 019: ID 10c4:ea60 Cygnal Integrated Products, Inc. CP210x UART Bridge / myAVR mySmartUSB light
Bus 001 Device 026: ID 10c4:ea60 Cygnal Integrated Products, Inc. CP210x UART Bridge / myAVR mySmartUSB light
Bus 001 Device 018: ID 1a40:0201 Terminus Technology Inc. FE 2.1 7-port Hub