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Hi Leon.
You can dark subtract with Registax, but I've not tried it before.
The order of processing should be something along these lines. Convert Raws to 16 bit Tiffs (including darks), combine your darks to created a master dark. You can use registax for this but I've never been very happy about how well it makes a master dark. Then, dark subtraction, flat subtraction (if using flats), aligned, optimized, stacked and waveletted in Registax. Save as tiffs again if your post processing program handles tiffs. Then reopen into your post processing package and complete your curves and levels adjustments.
Alternatively download IRIS (free) and download Jim Solomons Cookbook and give IRIS a go. Pretty steep learning curve but if you follow the Cookbook it will give you a good starting point.
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