I've recently set up two different macOS/OS X versions on my Mac in order to support running some legacy software. Each system is on a separate drive partition and my user account is on a third partition. I've mapped the my user account for each OS installation to the third partition so that documents and settings are available when booting in either system and I don't have reconfigure all of my settings.
On the surface that has worked. However, I've noticed a few peculiarities with settings that have changed. My guess is that going back to the older OS which might have different configuration format the default settings were generated and saved. And then when booting in the newer OS they were 'migrated' overwriting the settings in the newer OS. This seems to correlate with increased CPU activity when I boot into the newer OS after using the older one. But this is just a theory.
Are there any particular things that I should do or avoid specifically with this kind of set up? Or are there reasons that this is not a good idea and I should use separate user accounts for each OS installation?