I understand the frustration but if you’re willing to test it again sometime, Bazzite have really good docs that tell you all of that. Usually you want to use flatpak (using the app store, called Bazaar), if the software you want is not available there then you have other options like appimage, brew, distrobox and rpm-ostree (this is like dnf and apt, but it layers the packages since it’s atomic distro).

Scripts should just run like normal unless they rely on some tool not available by default (brew is usually used to install cli tools) or if it modifies something in a read only directory like /usr.

It seems like a lot but when you get the hang of it, it’s fine.

Oh and the Bazzite Portal app should help with installing the most common stuff.