on this matter i am little noob and prob really simple question with answer, but how i can add example ProtonVPN to start automatically when system boots up on F40 Silverblue? i gues i need to add Dekstop app file to somewhere and done but where?
You can copy or symlink the .desktop file onto ~/.config/autostart or use GNOME Tweaks (currently only available as a layered package) to manage startup applications.
Source that I referenced:
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thank you this was the solution and it works as mentioned only on Layered pakages is enabled that way i have some APPIMAGES but those not work but mainly i needed the VPN to autostart and it is done now
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Honestly, if it’s a layered package you need to start it should be programmed as a systemd unit or service. That is the currently “correct” way of doing it on Fedora Atomic versions.
You can but that is so not the right way. On Fedora Atomic, if you need to have something start automatically at system startup you should use a systemd unit file to set it up
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so copy paste works, but not recommended or correct way so how to do it as correct way on atomic to start it as systemd so i can do it now and later on other apps as correct way
I’m also struggling with this.
cp /var/lib/flatpak/app/com.discordapp.Discord/current/active/files/share/applications/com.discordapp.Discord.desktop ~/.config/autostart
but it doesn’t open on reboot 
That’s the wrong desktop entry; it’s the original upstream version that hasn’t been modified by flatpak to invoke flatpak run. You need the exported one in /var/lib/flatpak/exports/share/applications.
Alternatively, you can use GNOME Tweaks (as mentioned above) to do it point and click style.
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What terms do I need to search for to learn how to do this? I have an app I’d like to have running at the login screen. They have deb, rpm, and flatpak and it requires X (it shares keyboard and mouse between two machines). Do I install with the .rpm with rpm-ostree? install the rpm with toolbx? I’m a little in over my head on this one 
Probably “create systemd startup service” would work!
If you just want to run an application upon logging in then ~/.config/autostart is good enough. If you want to run any command during systemd startup then creating a systemd service would be the best choice.
Funnily enough, I don’t know how to create one yet :P.
Update: Oops I forgot about user services which runs on logging in for the first time :P.
Sure, but what’s available to me at that point? Can I run a flatpak? Can I load a toolbx? Does it have to be layered? 
Pardon me if I am and was wrong, because I am still learning things about Linux .
As for the ~/.config/autostart method:
Seems like that .desktop file is not the exported file. After some digging, the actual file is in the export folder instead of files. The command:
cp /var/lib/flatpak/app/com.discordapp.Discord/current/active/export/share/applications/com.discordapp.Discord.desktop ~/.config/autostart
Should work, there is also:
cp /var/lib/flatpak/exports/share/applications/com.discordapp.Discord.desktop ~/.config/autostart
Because the file is a symlink to the file in the first command.
Source that I read: Requirements & Conventions - Flatpak documentation
Maybe start here …Understanding and administering systemd :: Fedora Docs
Does that only work for things installed with rpm-ostree? Is there any way for it to work with flatpak or toolbx? For flatpak would I just call the executable from /var/lib/flatpak/exports/bin?
Check this link out then …https://www.redhat.com/sysadmin/podman-run-pods-systemd-services
You can try flatpak run <app name>. The name is pretty hard to remember so I often do flatpak list :P.