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If you know the maximum amout of graphs that you want you should be able to use the disabled property node to enable or disable the graphs as you need to. You can set up boolean controls for the individual graphs you want.
You will need to be collecting data from your maximum amout of channels unless you want to stop the task and reconfigure it for the right number channels. But that might get confusing if the user is given selectablity of individual graphs.
Possibly you should consider using the DAQmx Read N Channel N Sample 1D Waveform instance.
The Waveforms take the Channel Name attribute and automatically apply that to the plot name when graphed. You can even assign the Channel Names with the DAQmx Wizard.
