First step to take is to store a document in iCloud from within GoodReader.
Next step is to setup your Mac to use iCloud. You might need Mac OS X Lion for this to work.
The last step is to open the Library folder inside your Home folder. By default, this folder is hidden in Mac OS X Lion, but you can open it or make it permanently visible by using one of these methods.
Inside ~/Library you'll find a folder named Mobile Documents.
If all has been setup well, GoodReader's iCloud folder should be visible there. Inside that folder is a Documents folder. Simply drag a document into that folder and it is auto-synced into iCloud. You are then able to see the document in GoodReader's iCloud folder and download it from there onto your iOS device.
I have made an alias in my Finder window's sidebar to the Mobile Documents folder, so I have quick access to it.
