Transfering PDFs to ipad on windows

Put your PDFs in a folder structure on your computer, in DropBox, or on a computer somewhere online that you have FTP or SCP access to.

Then, in GoodReader, sync that folder. You can do it locally over WiFi and SCP or WebDav, remotely over SCP, or through DropBox.

Once the PDFs are in GoodReader, you can read them offline, mark them up, etc. If you set up bi-directional syncing, then when you are back online you can sync your notes back to your laptop.

You might not be happy with the current functionality of iTunes, but here's how to works. The folder structure from iBooks in iOS doesn't get reflected in iTunes, so you can't control which category new books will arrive in on the device.

You can have a folder of epub files and drag them into iTunes, but they go where iTunes puts them, not a folder of your choosing. This allows bulk injection of hundreds or thousands of books into management for syncing.

The computer version of iTunes will then make a copy of those files in it's Media folder and sync them to all iOS devices the next time they sync (assuming you have the sync rules to sync all Books to each device).

Now, the good news is that if you go ahead and file a book in a category on your iOS device other than Books, that information does sync back to iTunes and the next sync will re-organize things on other devices so you file once, and then sync each device to get them all in sync.

Furthermore, if you have a new iOS device (or erase an existing device) and push all books to that device. The folder status from the last device sync goes to that empty iBooks on iOS.

If and when Apple adds a control to iTunes, you may be able to order books on iTunes just like you can order App icons in iTunes and then sync the device to see the results.