I know you can SSH into your iDevice and make changes to some things... I'm in no way an expert w/ that process though. I believe, though, it's for customizing more than for adding/deleting items from your iDevice.
once you use it a few times you'll notice how simple and organized things are within iTunes. .... trust me i came from android and still do some ROM and app development for android and wished there was an android equivalent to iTunes.