The next stage (or the first stage, if you're not using a master bias) is to debias all your data frames; flatfields, flash frames, dark frames, and the targets. Debiassing can be done in two basic ways -- with and without a bias frame (well actually three methods exist, the third being subtraction of a constant; this is well worth avoiding unless there's nothing else for it). Let's tackle these methods one at a time.
CCDPACK