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The bad pixel file is good to use. Some hot pixels are not consistent in their response. By taking a long dark frame and selecting the hottest pixels you create a "bad pixel map".
IRAF and other professional reduction programs use this feature.
As for the original question, use the ISO you always use. I used 800 for my 40D as this gave the best dynamic range. There is an optimin ISO to use with each DSLR.
All changing the ISO does is to change the "gain" that the value each pixel reads is multiplied by. You want to use the full dynamic range of your camera. If the ISO is turned up too high you will lose the brighter parts of your image ie stars. The data for the dimmer parts of your image is still there at lower ISOs but needs enhancing using curves etc to bring it out.
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