I found a way to get BEs and U1s to run on the same machine at full hash rates using both versions of cgminer at the same time. I had to use in the antminer .bat file so it doesn't try and read any new devices. In order to have more than one U1 run at the same time I needed to hotplug each addtional one, to get around this I just run another instance of the cgminer (antminer.bat) for each additional U1 one at a time. After the ants are running then I can just plug in the BEs and start normal cgminer for them.

The only issue I have is when running all U1s together in one instance of cgminer, as opposed to one instance for each, it runs for only a few hours before it "stops working". I have no idea why.