Installation Location

Minecraft: Java Edition is stored in the ./home/minecraft/mc-instances/mc-INSTANCEIDHERE/ directory, it can be accessed via the Files menu for your game instance, or, sFTP/SSH.

Panel File Manager: To find your instances ID, visit the Minecraft:Java Edition > Instance Name > Files. The Files menu will drop you straight into your instances installation directory.
NOTE: The instance ID is in your browser URL, eg: "panel.creeper.host/TestServer/services/mc/mc-5c604c6ddc398/~~files~~files" when visiting any menu for that instance.

Files added to the instance's directory will be detected by the control panel for starting the server, Mods/Plugin Management etc.

An example of a healthy structure listing (Note: "Files" menu does not show the /home/minecraft/* part of the file structure):

/home/minecraft/mc-instances/mc-INSTANCEIDHERE/server.jar
/home/minecraft/mc-instances/mc-INSTANCEIDHERE/configs/
/home/minecraft/mc-instances/mc-INSTANCEIDHERE/mods/
/home/minecraft/mc-instances/mc-INSTANCEIDHERE/world/level.dat
/home/minecraft/mc-instances/mc-INSTANCEIDHERE/server-icon.png

Any files dropped into the /home/minecraft/ directory via sFTP/SSH will not be detected by the instances menus, they must be within the /home/minecraft/mc-instances/mc-INSTANCEIDHERE/ directory.