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You could think about it from the point of view that you're creating a mono greyscale image which represents the intensity of light at the wavelength you're allowing through the filter. In this case that's OIII ~500nm. So if that signal happens to fall across the green and blue channels then I would just combine them into a single mono image (in practice this usually means creating a normal 3 channel image where each channel is the same)
You'd do the same for your Ha and SII so you basically have 3 monochrome images which represent the light intensity at the 3 wavelengths (or wavelength ranges)
Then you can combine your Ha, SII, and OIII as you please.
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