CloudOn is a virtual desktop. It does not have access to the files on your iPad (to the best of my knowledge and the App Store description). You have to copy the files you want to work with to one of the supported cloud services (Box, DropBox, Google Drive).
In CloudOn you set up your account for that service, then you will be able to access those files. You also need to get the app (each has one) for the iPad.
Once you do that you use that cloud service to move files between the iPad and CloudOn.
I do not have CloudOn myself, so this is all based on the App Store description and various articles I've read; but it makes perfect sense when you know how CloudOn works. You are basically running a remote computer (instance on a server). Other than the screen interface there is no (deeper) link that makes your iPad's and CoudOn files available to each other. That's where the middle man cloud service, available on both platforms, comes in.