First of all, in Linux everyone should only use software from distribution repositories (eg. via apt command in Debian, Ubuntu, Mint, dnf/yum command in Fedora etc…). Package managers will install software in controlled way and it is really easy to remove them too. And, there is usually gui app for installing apps from distribution repositories.
Second way is to use flatpak / snap. They are pretty much similar and will keep things easy.
Do not install sh packages or tar.gz if you really do not know what you are doing. These are only for expert cases.
One fundamental change coming from Windows is that in Linux, you should never worry about location where software is installed (except for those expert cases, which you should not use). They will be put in correct places always. In Linux, apps are sorted so that executables go to /usr/bin, library files to /usr/lib64 and /usr/lib, applicatoin other non-modifiable stuff to /usr/share etc. It gets quite a lot to get used to, but in long term it feels more natural than Windows way to dump everything in app directory.
My recommendation will be to install some user friendly distribution (Ubuntu, Fedora, Mint) and just go ahead with default package management things what it offers. If you see Android way handling software good, Fedora Silverblue is kind of like that - System upgrades are handled same way, and applications are installed as flatpaks.
The C64 Mini and C64 Maxi are readily available today and affordably priced, making spare parts easily accessible.
If those work well enough for them, I cannot see any benefit of upgrading.