Using the control panel: console, SFTP, startup flags, schedules, subusers, databases and storage.
Day to day, most administration happens in the panel: the console, the file manager and scheduled tasks. For anything involving large uploads, SFTP is faster and more reliable than the browser file manager.
If other people help run the server, subusers give partial access without handing over your account. Scheduled restarts are worth setting up on any server running mods.
The panel is Pterodactyl and works the same on every tier. See what each Minecraft plan allocates.