1. transfer the files to your computer, and use iTunes file sharing to transfer them to the app you plan to use them with. See http://support.apple.com/kb/HT4094?viewlocale=en_US&locale=en_US
2. transfer them to your computer. Upload them to a cloud based file storage service like dropbox, box.net, 4shared, sugarsync or any other such service that is also supported in the app you plan to use the files in.
2b. open the app on your iPad, login to the online file service, and download the files to the app.
There is no general file system to transfer a file to on an iOS device - you need to transfer files to specific apps, so first you need an app that can work with the files you plan to transfer.