I usually image my RGB frames at 2x2 bin and luminance at 1x1. My usual process is to process the luminance image and save. Align all the RGB data and combine into a RGB image then process as usual. When I'm happy with both I'll open the finished RGB and Luminance image and use the Dynamic Alignment tool to align them. Use the luminance image as the 1st image (reference image) and the RGB as the 2nd image. After picking at least 3 point and they are corresponding to each image, drag the triangle button (new Instance) onto the RGB image. This will generate an aligned RGB image. Save the aligned image and then use the LRGB Combine tool to create the LRGB image. With the aligned RGB image and luminance image open, un-check the R, G, and B boxes. For the luminance box, left checked, click the right down button and you should see the luminance image listed. Choose that image and then drag the new instance button onto the registered RGB image.
I'd be curious to hear if this is any better, different or otherwise than the other procedures mentioned. Always good to learn.
Steve