This forum is for questions from those managing sites on iTunes U, Apple's service for colleges and universities to post educational material in the iTunes Store. You'll be most likely to get help with this issue if you ask in the general iPad forums. The iPad in the Enterprise forum may be most productive. You might also try asking in the Moodle forums:
I am using about 450 iPads to access resources and submit assignments on a Moodle server. We use MoodleEZ which is intended to allow one to upload files but this has not been successful in a Moodle 2.3.1 system. The only way I have been able to upload files has been through Dropbox. Add the dropbox repository to your Moodle server and students can submit any file that is stored in their Dropbox folder. They can place files into Dropbox with iOS 6.x and the current versions of Pages, Numbers, Keynote etc. Many other good Apps have the option to Opne in.. and choose an App. Upload to Dropbox and then submit from there. Not a great solution because it is bandwidth intensive in a school / university situation. If you have a WebDav server that allows access to the student home drives that would work better but I do not manage our Windows servers...