Image pre-processing with Pixinsight - calibration and registration

Important: I'm still new to Pixinsight. The instructions below are my current, very incomplete understanding of how this works.

Now, where I started using Pixinsight for post-processing, I also want to figure out how to use it for calibration, registration and stacking.

Before calibrating images, I need to create masters (dark, bias, flat). Pixinsight has the ImageIntegration process that can do that. I decided instead to use the BatchPreprocessing script that reads all the calibration frames and creates masters on the fly - and re-uses them later.

I'm adding Bias, Darks, Lights and Flats with the "+" buttons at the bottom. Bias and Darks are straight forward. But flats is trickier. I took my lights on two different nights and took flats both nights too. Which means I will have to calibrate both nights individually to use the right flats.

So, first the lights and flats for the first night. I select my first image as the reference image (have to remember to use it for the other filters too, so that all subs are aligned properly). I created a directory ("processing") to store all the intermediate frames. Have to make sure that "Image Integration is not clicked as I only want to calibrate and register". Finally, I clicked on the "Diagnostics" button that checks if everything is setup correctly:

Click "Run" ... and wait ...

Many minutes later, it's done (weird, no success message or such - you know that it's done when the process console disappears again).

In my processing directory, Pixinsight created three directories: master, calibrated, registered. In the master directory are the calibration masters stored:

In the calibrated and registered directory are all subframes stored. Pixinsight added a '_c' for calibrated subframes and '_c_r' for calibrated and registered subframes.

Next, I want to calibrate and register the subframes from the second night. After the first run, the checkboxes for "Use master bias", "Use master dark" and "Use master flat" are checked for subsequent runs. Which is fine for bias and dark frames but not for flats as we want to use the flats from the other night. So, I remove the light and dark frames and load the frames from the second night. I needed uncheck the "Use master flat" checkbox before loading the flat frames - otherwise Pixinsight would treat every flat subframe as a new master. Again, I have to make sure to keep the frame from the first set as the reference frame, so that all images are aligned.
This time it didn't take that much time as the dark and bias masters were already created.

Now, I had to do the same for the green and blue filter. Actually, the script can automatically sort by different filters. Have to remember to uncheck the "Use master flat" checkbox again! So, I'm loading all my green and blue flats and lights (you can see in the screenshot how Pixinsight separated the blue and green flats):

Quick check with "Diagnostics" to make sure that I didn't forget anything - and "Run".

After it's done, I have the following files in the master directory:

The bias and dark master and one master for each filter (the script overwrote the red master from the first run). And in the registered directory I have three directories: blue, green, red.

Now, where I'm done with registering, I can move on to stacking.