The easiest way to transfer files to your Linux server is by using SSH/SFTP client that acts as a file browser.  To get started, please follow the steps below -

1. Download CoreFTP on your desktop by visiting http://www.coreftp.com/download.html
2. Once CoreFTP is setup, run the program and in the site manager fill the following fields -
   1. Site Name - Here you can enter the server IP address or hostname
   2. Host/IP/Url - Please use server IP address
   3. username - root
   4. password - please under the password for root username
   5. Port - 22
   6. Connection - SSH/SFTP
3. Click on connect and it will provide the key for secure transfer.  Accept the key and you are not ready to browser the server directory and upload/download files.