RemasterDog makes a remaster of the full system "/", including changes and loaded extra modules.
RemasterCow (COW=CopyOnWrite) makes a module from the save-folder or save-file.
I'd say use one or the other, not both, probably your 01-remaster.squashfs has already the changes included same as in 02-changes.squashfs
Not sure what you mean. Why would it ?I suspect when using 01-remaster.squashfs the OS will run on this machine only?
Yes, the 02-changes.squashfs has the changes already, so it would be waste of space if you keep the old changes.When copying e.g. 02-changes.squashfs to the location of 01-filesystem.squashfs shall I remove everything from directory 'changes' before doing a reboot?
I would not remove content of 'changes' while running the system, there's Menu entry "Clear changes at reboot", better use that.
There's more to say about this all, it's a bit late here, so keeping it short.
I admit it can be confusing how to use these options. (BTW, there's also "Quick-Remaster Gui" which is more convenient to use then RemasterDog)
P.S. I wouldn't recommend using RemasterCow (and loading e.g. 02-changes.squashfs) if your changes contain installed programs with apt-get or synaptic, specially if you kept the checkbox checked "Disable dpkg registration", then the package management doesn't know about these programs.
(for personal changes, added files, configuration etc... it's OK to use it)
Fred