First, to clear up some misconceptions, using FTP is not "bad for your files". If you use it, your files will arrive at the server unaltered and in good condition. While the FTP protocol has a laundry list of issues, the main problem is that it doesn't use any encryption. As such, both your username/password as well as your files are sent across the network in cleartext.
Is this a linux server? If so, you should look into using SCP. SCP uses SSH as a transport, and chances are good that you already have an ssh server installed and running, so it wouldn't require any additional work on your part. When using SCP, all of the data in transit is encrypted, including both your credentials as well as the files you're transferring.
Depending on what client OS you're running, WinSCP or Filezilla both support SCP and will provide you a nice GUI.