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Matt, it's all going to depend on what software and wheel you use - I don't think there's any general guide that would be good enough.
But the principle is easy enough - just do what you're doing now, but 3 or 4 times in a row (3 if you're doing RGB , 4 if LRGB) with a different filter set in each run.
I don't know if there's any software to automatically name each run according to the filter (and how would it know anyway which filter you're using?). I ended up writing a bunch of custom stuff to do this on my setup since I couldn't find anything.
I'd suggest it's as easy as doing the runs in a set order. Anyway, each of these channels looks so different that it's hard to get them mixed up :-)
regards, Bird
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