A good way to check your disk usage for folders on your Linux server is via shell.
- Download Putty.exe for this location http://the.earth.li/~sgtatham/putty/latest/x86/putty.exe
- Open the program, in the 'Host Name' type in your IP or Domain name and click 'Open'
This will list the folder and sub folder size as well as the total size of your root directory structure.