I’ve ran into an issue where when I add Manjaro to Multisystem it overwrites the existing Manjaro distro on the drive. This is because it always creates a folder called “manjaro”. To get around this we need to change some names. First add the distro to the drive. Rename the manjaro folder to something else. Since I was using LXQt I changed the folder name to “manjaro-lxqt”. After doing this you need to update the references to the folder in the grub.cfg. Since it adds an entry for free and nonfree there are 6 spots that need updated total. The entry below is the nonfree entry and the red text is where I updated the path.
linux /manjaro-lxqt/boot/x86_64/manjaro misobasedir=manjaro-lxqt misolabel=MULTISYSTEM nouveau.modeset=0 i915.modeset=1 radeon.modeset=0 nonfree=yes logo.nologo overlay=nonfree quiet splash showopts
After updating grub.cfg, update grub then you can add the next Manjaro spin. It will also create a folder called “manjaro”. You can continue adding versions as long as you update folder names and references to them. I typically rename even the last one I add just incase I want to add another one down the road.