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Typically DSLR use RGGB bayer matrix and it works fine for processing my nikons.
FITS try 32bit, the stacked image contains all the data from your photoset so keep it at the highest bit depth possible for more flexible processing options. But unfortunately I've found many astrophotography programs dont support all FITS formats, so you might have trouble with going from one to the other. I work entirely within PixInsight for stacking and processing tripod dslr shots, so I dont know if this problem will arise for DSS -> StarTools. Failing that, if you can use TIFF, again 32bit if possible. Rational vs integer, try them . Basically try them all to go from one program to the next. The file sizes should be big containing all the data from the images, if you go to 16bit instead (or worse 8bit) you are throwing away data. The stacked image will probably look black at first, stacking alone doesnt make a nice looking image. You need to then stretch the image and work on it to bring out the colours and details.
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