If your data set includes different rotation angles, then you have two possibilities:
(a) Calibrate your frames in separate batches, one per rotation angle. Note that your master bias and master dark frames will be generated in the first batch, if necessary, and you can reuse them in the following ones. Only the flat and light frames are rotation-dependent. Use the same registration reference image for all batches.
(b) Use pseudo-filters as follows:
1. Click the Add Custom button.
2. On the Add Custom Frames dialog, select your light frames for a particular rotation angle. Select: Image type = Light Frame, Filter name = 180DEG (for example), binning and exposure time as appropriate. Click the OK button.
3. Repeat step 2 for your flat frames with the same rotation.
4. Repeat steps 1,2,3 for as many different rotation angles as you have.
Now your light and flat frames will be grouped by the pseudo-filters specified in step 2, and the script will generate separate master flats, which will be applied to the corresponding lights.
Irrespective of the method you use, you should integrate all the registered frames *after* running the BPP script. Remember that the integrated results (the master lights) generated by BPP are only useful for fast previewing purposes; image integration must always be done manually with the ImageIntegration tool.
My software (CCDAutopliot) apparently writes the rotator angle to the FITS.
There are no standard FITS keywords for this purpose. The solutions given above work without problems if you have your files well organized. However, a future version of BPP will allow you to enter custom keywords to classify frames, which will simplify even more the process in these cases. We have other priorities right now so don't hold your breath.