Heya theghostsong, it's best for technical questions like this to first be asked via tcadmin support ticket, we are able to help you quicker there.
You can use the drag and drop method via filezilla, or you can zip up all of the mod files if they aren't already zipped and then upload them via filezilla to your game server. TCAdmin can then unzip the files for you using the filemanager. If they don't unzip to the correct location, filezilla allows you to move the files around without re uploading them (very cool).