Hi cd384-
In general, you can have two (or more) DAQ Assistants in the same VI. I assume, however, that you're trying to have separate DAQ Assistants for analog input and this definitely will not work. You must group all tasks of the same type (analog input, analog output) within the same DAQ Assistant or DAQmx Task. You can add multiple channels by holding control and selecting multiple items when you are initially configuring the DAQ Assistant.
In order to separate signals in LabVIEW you can use the Split Signals function that is available on several palettes. To find it, just click "Search" from the functions palette and search for "Split Signals"
Thanks-
Tom W
National Instruments