• ends up asking on reddit
• zero upvote, gets one answer three days later

gonna chalk that one up to reddit

• learn there are two folders, one is in the system the other in home

This is not an immediately obvious thing, but consider this a learning experience. This is the way many things work on Linux. As much as possible, you want to let the distribution manage the files outside of your home folder (occasionally you might tweak some system-wide configuration files). It is possible to install all sorts of software and make a lot of configuration changes right in your home folder, without admin privileges (in other words, without having any impact on other accounts which share the machine). The distro package manager should be the first stop, but if you find yourself DIYing something because a package is not available for your distro, there is almost certainly a way to do it without raising privileges (or if you need to raise privileges, doing so to grant access to specific hardware, or to enable a service on start-up, not to just shit files all over the place and forget about them).

In the case of .desktop shortcuts, you can drop these in ~/.local/share/applications. (more info)

In fact, I realised waaaay too late that the home folder was "~".

Yeah, this is a shell expansion. You can test it by typing echo ~ in a terminal. It is a shorthand for typing /home/myusername or $HOME. This dates back to at least the 80s, so the syntax is also copied by a lot of non-shell applications or even used in some documentation outside the context of using a shell at all. In a shell like Bash you can also use it as a shortcut for other user's home directories by typing e.g. ~root instead of ~. Good thing to know, as it will be taken for granted in a lot of places.

everytime I saw a folder path starting with ~ I assumed it was some convention

You're weren't wrong