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If you must use darks for your flats (Not required) treat them as bias files. Really at the calibration step in IP the requirement is for Bias files to remove the read noise from the CCD snd it's electronics. The read noise will be captured on these darks but be aware that any imperfections or hot pixels etc captured during this process will be largely very random and may well impart some iof these imperfections into your lights during the process.
Probably a more important part of the process is the stacking method used for your lights in the final part of the process. This can remove or reduce a lot of minor abnormalities depending on the quality of your lights.
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