You usually manage files stored on iPad using iFunbox on your desktop. This app is available for both Mac and PC and lets you upload files from computer, extract files from iPad and so on. This way you will be able to make backup of information stored on your iPad.
The iFunbox lets you see system files which are not visible otherwise on iPad. This functionality is important as the iTunes does not allow you to peek into the system and program files which are required if you are into iPad game hacks and cheats. This also helps one to get rid of useless and junk files.
With iFunbox you will also be able to install the usual IPA files which are basically setup files for apps. You will also get the ability to import or export media data. The iFunbox is available for both Mac and Windows operating systems which is great as you can install iFunbox on both and use the iPad as USB flash drive. You can store all of your normal data in “General storage” and this can be accessed on both Mac and Windows computers. Download iFunbox from here.