I used OneDrive, and especially the file on-demand (all files on server visible in explorer but only downloaded when needed) feature a lot
You can continue to use OneDrive. I use the OneDriver client and it works really well - your drive appears just like a local drive, but files only get downloaded when you try to access them. Once downloaded, it gets cached locally and is available offline, and is kept in sync automatically. Other cloud providers should have similar FUSE clients available.
What are best practices for managing apps?
Best practice is to stick to packages provided by your distro’s repos. Flatpak should be your second option if you can’t find your app there, and AppImages should be your third option (since Flatpaks are superior as they can share dependencies, unlike AppImages). Avoid Snap. In fact, avoid any distros that even use Snap (*buntu). Also, if you’re on a Debian/Ububtu based distro, avoid adding PPAs (thirdparty user repositories) as far as possible, as these can cause dependency issues and may cause pain when you upgrade your distro.
Is there a GUI (I know) way to see all applications
That should be provided by your distro - Gnome-based ones have “Software” and KDE-based ones have “Discover”.