The iPad file sharing system Apple implemented is rushed, and flawed. If you still haven't tried it, you're basically forced to plug the iPad via USB, open iTunes, select an app that supports this feature, choose a file from your computer and copy it into the app database. This is not a sync, it's a Mac > iPad file sharing, and it's broken and slow. MacObserver has a great and insightful article about it.
Fortunately some developers are thinking about a solution for this, and I've come across this application called "Folder" in the App Store which has turned out to be pretty useful.
The concept is simple: instead of having to deal with dozens of different applications that supports dozens of different file types, you just throw everything into an app and then - on the iPad - you decide where each file has to go. You don't have to deal with iTunes anymore, you just copy all the files into Folder and then you move the files around. You can also forward email attachments to Folder.
Folder is useful, but it's a little bit pricey at $2.99 [iTunes Link]. If, however, you think this might be the ultimate solution for your problems, give it a try.