That's right, Martin. Normally, the flats have much shorter durations than normal subs - so the standard dark frames can't be used.
At that point you have two choices:
Dark optimisation - that essentially scales the standard dark to try and match the exposure time of the flat. So if your dark is 200s and your flat is 2s, it would generate the dark for your flat as (dark - bias)*2/200 + bias.
No dark optimisation - it just uses the bias instead.
Which one is better depends on how your camera works - your camera dark current would need to be linear to use dark optimisation (DSLRs are notoriously non-linear - camera designers do all sorts of processing, even for raw frames. These make sense for standard photos, but not for astroiemagers).
You can also try taking dark flats - darks which match the duration of your flats and see if that makes a difference.
Personally, I would just stick with using the bias (no dark optimisation). You shouldn't get much more than one electron or so of dark current for your flats, and this will compare with ~ 20,000 electrons for your flat signal, so the noise is minimal.
Colin
