I was asking more what program you were trying to make .desktop files of, I should have been clearer, sorry for that.

I thought you were trying to make shortcuts for already installed programs on your desktop. If that were the case, on KDE at least you could just right click a program on the start menu and click to add it to the desktop.

But I totally get your frustration, the two locations for storing configurations should be communicated better for new users of Linux.

As a rule of thumb, most of the time you can always put configurations on your home folder, an example of this is if you need or want to mess with Pipewire configurations (system audio application), where instructions on the internet will tell you to put it somewhere with root access, but in reality you can just put it in a specific place on your home folder too, which is way easier.

And yeah, ~ always points to your user directory, it's another one of those Linux things that are common knowledge, but that new users aren't told about until they stumble upon it and have to search for.

Another way of specifying user directory without using your user name for that occasional application that for some reason doesn't accept ~, is to use /home/$USER/ in case you ever need that.