I think the first thing is actually recommend is enabling a daemon that launches Plex at boot without login. sudo systemctl enable plexmediaserver For something like a Minecraft server I'd recommend reading up on the setup process. (It's a fair bit to summarize)

If the application doesn't come with a systemd service I'd recommend making a cron. They're scary looking but actually pretty easy to use, I use it for automating maintenance on my server.

It may feel counter intuitive but Linux servers don't really need a desktop to manage them so most the tools don't really come with graphical apps. If you want an interface to check on things I'd recommend installing and using cockpit web based graphical interface.

If you want to do it proper on a systemd system make a systemd.service it's not as easy to learn but you get extra tools to manage it.

I've heard there's a lot of work that has been done in kde and gnome to get rdp (remote desktop protocol) with remote login.

I hope this helps! If not, almost everything can be done through the terminal and ssh(secure shell) makes that process really easy. I installed and setup my Linux laptop and my server that way.

If you just want to transfer files there is sshfs(secure shell file system) and the ability to go to your file browser and type in an sftp(secure file transfer protocol) address. In kde dolphin for example you select network and type in the bar sftp://(IP address or hostname)@(user):(working directory). Make sure you have sshfs installed on both machines and sshd enabled on at least the system you want to access.