Hi Andy. Welcome!
When you load your new bias, dark and flat frames in BPS it will create master frames and save them in the master folder created in the chosen output directory. To reuse, just load them into their respective tab and check the master frame boxes.
Because PI normally uses dark scaling, the bias is subtracted from the darks as a rule. This is different from some other programs. However, you can choose not to if you wish, by using the stand-alone ImageCalibration tool. I will have to refresh my memory as to whether this can be done in BPS.