You do not manage Unix permissions on our servers. Every file is owned by the user your server runs as. Errors you see are about something else:
"Disk quota exceeded" / "No space left on device"
Your server's disk is full. Delete old logs (logs/ folder), old backups on disk, unused world folders or leftover zips; or upgrade the disk in the dashboard. A full disk also prevents the server from saving the world, so fix it before restarting.
"Permission denied" when unpacking or deleting
Usually a file that a running process holds open (the server writing to the world, or a download still in progress). Stop the server, wait ten seconds, try again.
"Cannot open file / access is denied" from Wings
The panel's file daemon refuses paths that leave the server folder (../) or symlinks pointing outside. Keep everything inside the server root.
"File too large to edit"
The browser editor caps at a few megabytes. Download the file, edit it locally and upload it again. If it is a log, read it with Kowalski, which searches instead of loading it all.
The world folder does not appear after upload
Refresh the file list. If it is inside another folder (world/world/level.dat), move the inner one up one level and delete the empty shell.