One procedure is to first calibrate your raw Bayer CFA, then de-Bayer, extract channels, and run the script on each channel separately. The default parameters are usually OK, but there are situations where changes are needed, such as when SNR is low and the script doesn't detect enough stars. If your optics have annoying aberrations near the edges, you can crop the channels and focus on only central region measurements. Stronger gradients and atmospheric scattering due to clouds and dust can sometime result in less useful measurements, I like to use Blink to find these problems.
Mike