There’s no one “proper” way. Running multiple DEs shouldn’t break anything, but each DE comes with it’s own set of dependencies and other software, so it does add clutter. There will also be considerable overlap with config files, so if you change a setting in one DE, it could change settings when using another DE.

Having a separate user account per DE will prevent most of the configuration overlap, but it doesn’t solve the abundance of packages you’ll have installed from having multiple DEs. I don’t think there’s a great “clean” way to do it.

One thing I love about Linux though, is how relatively flexible the user home directory is. When moving to a new distro or PC, usually everything you need to copy over is within your home directory. For what you’re trying to do, I’d consider throwing /home on a separate partition. That way, you can try out multiple DEs and distros, without blowing away your home folder. And you’d be surprised at how small your root partition can be, the vast majority of your storage should likely be reserved for /home. The Steam Deck, for example, uses a root partition that is only 5 gb. On a typical Linux system, I’ve found 64 gb to be plenty for root.

When switching distros and/or DEs, consider cleaning out various config files in your home folder. Almost all of them will be hidden files that have a filename that begins with a period. I only keep specific config files for programs I want to retain data for, like Google Chrome (.config/google-chrome), Thunderbird (.thunderbird), and Steam (.local/share/Steam). If you use SSH keys you’ll want to keep your .ssh folder too. But deleting all other config files will give you a pretty clean start when changing DEs.