The On-Air software will only capture one stream.
It will take one input from each card and allow you to choose which stream you want during capture. So an example would be: You have an input into each intensity (so two) and both inputs will show in the display app. You can then choose to capture and the stream that is selected will be captured. Then during the capture you can toggle to the other stream and record that into the same file.
So at the end of the capture you will have one file and it will contain data from the streams that were selected at the time.
Does that make sense?
If you need something to capture more streams then you will need to find an application that can support multiple Direct Show/Quicktime boards. Or if you know someone they can write the app with our SDK (but that is generally beyond most peoples means).
I hope that helps clarify
Sincerely,
Joshua
Director of Support
Blackmagic Design Inc.