Is there a way to control gain at runtime and to control the gain separately for each input channel?
The first part of your query: You cannot change the Gain set on a channel at 'run time'(while an acquisition is on).
You have stop the acquisition, reconfigure the cahnnels in the scan list for different gain and start acquisition
In LabVIEW, you have to specify different high-low limits for each channel in the 'Create virtual Channel' vi to set each channel at different gain. Look at attached vi to get an idea