jma_sp: you are right that if you apt-get install things, after OTA update they might be gone, but if you want to be sure, keep your data and software under your home folder. This is also why you want to intall your apps under your home, and keep your .desktop launchers under ~/.local/share/applications instead of /usr/share/applications.
Also, if you create a container, you create it under your home, so it remains and also it does not use up your firmware partition space.
I am committed to finally make a neat documentation this Sunday, so be on the lookout. I will definitely share links here.