The recommended method for uploading folders is via SFTP. A guide on this can be found here.
Alternatively, you can use the method below:
1. On your local computer, compress all the files and folders you want to upload into a zipped file.
2. Log into the Pterodactyl panel and open your server
3. Head to the Files Page
4.Use the file manager to upload your compressed file.
5.Once uploaded, unzip the file to restore your files and folders in their original structure.