Hi Ross
Best way to do it is to use a light box. You take your light frames and then immediately after, so camera orientation and focus are in exactly the same position, run off your flats. It takes no time at all to do and, as Paul has already indicated, it will remove your vignetting and any dust spots and other imperfections.
If you are after a light box there is a really nice guy in Adelaide, exfso on the forum see the ad in the classifieds, who will make them at a very reasonable price. I have no affiliation just a satisfied customer. Of course if you have the ability and the tools you should be able to make them yourself. I don't so I bought mine

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All the best.
Wayne