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Bayer is the filter just over the top of a one shot color camera chip be it a ccd or a dslr usually in a 4x4 pattern of red blue and green green, the green being diagonally opposites. It varies from camera to camera. Each pixel then records it's color and makes up the real color using pixels immediately next to it, theoretically this degrades the resolution, although generally it's not that noticeable in a print.
Quite frankly when I started using a dslr the RAW tended to go weird, so I just used ( in my case cannons software to decode it into a TIFF file) I found this the easiest and failsafe method of doing it.
So in conclusion change all your RAW files into TIFFs then stack, just label darks etc so there is no confusion.
NEVER shoot in JPG as the bit depth is too shallow to stretch much, jpg is for the final posting or print,
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