your assumption is correct - the BPP script is going to leave you with master bias and dark frames, a master light frame (the integration) and a whole slew of subexposures: the calibrated subs, the calibrated & debayered subs, and the calibrated, debayered and registered subs.
if your 2nd BPP did not use the same registration reference image as you used in the first, your two master lights are not going to be registered to one another. if that's the case, you can either register one of the master lights to the other, or re-run the 2nd BPP using the same registration reference that you used in the 1st BPP. or you can use StarAlignment to manually do this by loading the reference frame from the first BPP run as the reference and adding all the debayered subs from the 2nd BPP run as the target images. then integrate the resultant registered frames using ImageIntegration.
then once you have the 2 registered master lights, load those two master light images twice into ImageIntegration (II should be reset first as the defaults are fine for integrating masters). you have to load them twice because II requires 3 or more images.
rob