If you don't wish to click the link, here is the how to get it work.
This method use iNdependence 1.2.1 and everything seems working fine:
Step 1. Make your ringtone to m4a file. You can convert it easily by right-clicking the file from iTunes and choose ‘Convert selection to AAC’
Convert files to AAC first
Step 2. You will see a duplicated files in iTunes, that will be the AAC files. Select the AAC files in iTunes, than choose ‘Show in Finder’.
Make the AAC files shown in Finder. Copy it to the desktop
Step 3. You will see your converted m4a files, copy it to somewhere else. I copied it to MacBook hard disk.
Copy the AAC files to desktop
Step 4. Open iNdependence, quit all the iTunes stuff. Choose ‘Customize’, than choose ‘Ringtones’, and ‘System’. Click ‘Add’ to add the file you made in Step 3.
Use iNdepedence new version to add ringtone
Step 5. Restart your iPhone by pressing the Power button, slide to power off and power it on again. You will see your custom ringtones.
You will now see the custom ringtone
Although this does not have the ability for you to choose which ringtone you would like to sync, but I think this at least make your iPhone not just having those default sounds.