So long as you drag and then drop an Item to an area where the Background skin exists, this should build up, then the Reorder dock items can be used to set the items to and order that is appealing to you.
All settings are saved Live.
if you would wish to have a back up of your settings.
there is a couple of options:
You can go to the Config.xml and make a copy of this. This will be located in the AppData file in CD is a full install or in Circle Dock > System > Settings file if portable.
Teh other option is to create an empty file and Use Circle Dock settings to create a Portable App Backup of the entire build.
This is in settings > General > Portable app
Apologies if I am not making too much sense, I am exhausted
Let me know if these suggestions are not working