after normal bias/dark/flat calibration, Debayer using the Superpixel mode (not VNG) - this prevents the blue and green "noise" from polluting the nice clean Ha data. Then use rgb channel separation to discard the b and g channels - then register and integrate the "red" (mono Ha) images.
The superpixel mode reduces the image size in pixels by 75% for obvious reasons.
With Oiii you can do the same thing but this time you need to discard the red and keep the blue and the green (oiii overlaps both)
Sii is the same as Ha (keep the red)