Hi Tom,
There's no straight answer here, as far as I can see.
A lot would have to depend on the exposure times you are using to acquire your flats. They longer they are, the stronger the argument would be for then calibrating the raw Flats with a MasterDark.
The only way you would really know is to take dark frames at the same exposure time as your Flats, and then analyse your Darks. If there is 'area-specific' or 'zone-specific' noise present at, rleatively-speaking = short exposures, then you may need to use a Master Dark to eliminate the noise that must therefore be present in your Flats as well.
And the same argument applies to Bias frames as well - except that you have nothing like a 'dark' frame to calibrate them with, and nor do you need to trouble yourself with flats. Neither of these matter, because Bias frames are, by their very nature, 'zero-length' exposure images.
However, grab a healthy collection of them and perform a simple 'stack' (to create a Master Bias) - and then have a good look at what yyou are getting.
How do they compare with your Master Dark (a stack of a series of un-calibrated Darks is what you want for this comparison). If there is little difference between the two (on my QHY10 OSC camera, I can't tell the difference - even at 1800-second exposure times for the Darks), then you really have to ask yourself the question, "Do I really need Bias Frames at all, in fact - do I even need Darks?". After all, if you can't tell the difference, then you might as well just use Bias Frames in place of Darks - they tale a lot less time to acquire!
Would you let CCDSoft do partial frame calibration automatically? Or would you prefer to do this in PI? Well, that depends on whether you are prepared to fully get to grips with image calibration, and the extremely powerful tools that are available to you, under your full control, in PI.
If you are not happy with 'getting your hands dirty' doing all of the calibration stages yourself, then you might as well lett CCDSoft do things for you - and its not just CCDSoft in the frame here - even the likes of Nebulosity will doo all of this for you, leaving you with just the post-processing stage to complete in PI.
Will these other packages do things as well, worse, or better than PI? You have to understand the steps involved, and how your specific equipment performs, before that question can be answered. Just remember that PI has had some not insignificant effort put into its development, to ensure that what it does do, it does extremely well.
I know which package I rely on for image calibration (but I also run my images through Nebulosity - as I acquirethem - to give me a first glimpse as to what the final data might yield under all the statstical analysis of the PI engine.