Hi Phil,
You shouldn't have a problem communicating with the GPIB-USB-B and the DAQPad 6016 at the same time at all, even if the data acquisition task is still running. Data acquisition and GPIB communication are two totally separate processes, and assuming you have the two devices plugged into two different USB ports, you should be able to combine them in the same program without having an issue, just as if you had a PCI-GPIB card and a PCI DAQ card.
If you are running into problems trying to do this, let us know what error you're obtaining and we'll help you work through it!
Have a great day!
john
Applications Engineer