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It doesn't matter what colour it looks - it's the wavelengths that it passes through that makes a difference.
Still blend them as RGB.
You may still need to weight each colour when combining, or simply use levels afterwards, to adjust the colour channels independantly. In some conditions, some channels will be fainter and will need more of a boost in processing to even it out.
Ideally, you should set the capture settings so that each colour channel has the same peak in the histogram. This can mean capturing the blue channel at a slower framerate, or using a higher gain. It will be much easier to balance the colours later if you do this.
Great to hear you got the colour filters - what filter wheel have you got?
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