There are two things that you need to do to sort this out.
First of all, to sync Apple products, apps etc. you need to sign up to iCloud on all your Apple devices. Then you will be able to have books within iBooks synced up between your iPhone and iPad3.
Settings>iCloud>your icloud account details.
For syncing other non-Apple files etc. like pdf files, you can use a cloud-shared folder on each of your devices. That way, when you put a file into one of the cloud-shared folders, it will automatically appear on all your devices. This will also work for whatever laptops / desktops you have and will also works across Windows, Mac, iOS, Android etc. Each device can have it. My favourite system is Dropbox and you can sign up for a good amount of free storage here - sign up for Dropbox.
Good luck with this, it is what I do and it works very well.