Bill,
Once you have registered both sets of data to a sub from the high resolution camera, you can treat all the data the same.
Before using the NBLRGB script, try just integrating all the data together, it may give the result you want. If that does not work out, integrate the set of subs with better Ha signal, extract the red channel. Then integrate all the subs from both cameras as I indicated at first, then use the NBLRGB script to add the red channel with the better Ha signal.
Mike