Hi SG,
There is no way to accomplish this using the DAQ Assistant, since the channels are hard-coded in. However, the more advanced DAQmx API VIs do give you enough flexibility to accomplish what you want (located in the Functions Pallette under Measurement I/O >> NI-DAQmx). The DAQmx Create Channel VI takes in channel strings as an input, which allows you to use the Prompt User for Input Express VI. See the attached VI for a quick example.
If you want a "fancier" popup for the user, you could get creative and design a subVI to act as a popup. This way you could create lists to choose from, buttons, etc. to suit your needs.
Thanks,
Justin M.
National Instruments