If you want 2 separate Linux installations sharing the same /home partition for easy backup and restore the procedure in outline is this:
- Install your first Linux with separate /, swap, and /home partitions at a minimum. Other partitions are to your taste and experience.
- Create a user name for that installation, possibly one which acknowledges that it points to the first installation. Enter your password, etc. and finish the installation.
- Begin to install your second Linux distribution. Create a separate / partition in the remaining space on your drive. Designate your existing swap and /home partitions to be used as designated as the same on your second installation, but tell your installer not to format these partitions as part of the installation, while formatting the / partition.
- Create a second user name different from the first to reserve a separate space for settings/DE/data which would be kept separate, entering password, etc. to finish the installation.
- If desired, create symbolic links between the (visible) folders between the two users so that they are effectively one user for everything except creating new folders inside their /home/<username>/ folder and their DE, applications and settings. You will have to install applications for the two installations separately. If they become out of sync, you can use the terminal command dpkg -l (lower case L) to list the packages from the installation you are presently signed in to the same package list from your other distro.
- This will not replicate your settings between the installations, but that is the problem you found which make you post here. Replicating the settings can get you into trouble.
Using this method, you could, for example have MATE on your 32-bit installation and Windowmaker on your 64-bit installation with separate menus, backgrounds, etc. but still share the same documents, download folder, pictures, music, etc.