Workflows for STC Astro DUO Filter  

I have a STC Astro DUO Narrowband filter and was wondering whether anyone had any suggested workflows for processing data obtained using this filter and a OSC camera.

There are at least 2 ways I can see that this data might be processed:

1. Use the Ha-OIII color debayer algorithm and treat the data as a standard RGB dataset
2. Use the Ha-OIII mono, Ha-OIII extract Ha and Ha-OIII extract OIII algorithms to separate out mono (luminance?), Ha and OIII datasets for processing as bicolor or HOO

Method 1 above is pretty straightforward and this is how I have processed data so far.

What I am much less clear about is how I would use method 2 to generate separate but registered integrated mono, Ha and OIII files that could be combined using the combine tool or using other software? Any suggestions would be most welcome. At the moment, I can only think of selecting one of the debayer algorithms (e.g. mono) and running through all of the processes. After integration and the resulting file is saved, restart the whole process using the next debayer algorithm and repeat until all 3 files are saved. These may then need to be read back in for a final registration to make sure all are aligned. Is there an easier way?