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Hi Sadia,
This actually depends on the type of data you've got.
If they're monochrome images, then calibrate them separately (Darksubtract, flats etc.). After this I combine them all together using CCDStack.
In fact in CCDStack if you've got a full set of darks flats and bias frames you can calibrate them together as well, as the software will adjust your darkframe.
If you've got one shot colour images this may be different, and the HDR or layering techniques seem to be the go. Also CCDStack doesn't like the large images from DSLRs much, it runs out of memory, even when you've got 6Gb installed...
Cheers
Stuart
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