First, I don't recommend using iTunes to sync you iPad, computer, and iPhone. If you've turned on contacts, calendars, etc syncing in iTunes go ahead and turn it off. If you follow my following advice, be certain you turn them off, as having both local and internet syncing turned on at the same time will cause problems.
Instead, choose your service (be it iCloud, Google, Yahoo, Hotmail, or other) then sync each device and computer to that service. I works much better than using iTunes to sync.
You'll use the same Apple ID and other accounts on both/all devices.
As far as syncing your other stuff, like music and apps, you can use iTunes. It will remember what the settings are for each device. There may be occasional glitches where new songs or apps will sync unwanted, but removing them directly, from the device they are not wanted on will correct the issue.
If you choose to keep syncing your contacts and calendars through iTunes, and there are arguments for this; you need to keep in mind the limitations.
Syncing is not immediate. Devices and the computer may not be completely up to date with changes made on other devices and/or the computer. Each address change is incomplete until every device and computer has been synce after the most recent changes/additions/deletions.
If changes happen to the same contact or event in more than one place you will end up with conflicts that must be resolved.
Occasional duplicates are to be expected. The nature of having information on more than one device and large time gaps between syncing means that sometimes things get confused. In these cases it almost always means the system decides to keep both versions of a contact or event.