Hi
As a new owner of an iPad, I'm certainly not an expert, but I went through this trying to get my iPhone contacts into my iPad. I ended up with some contacts being duplicated up to 10 times!
If I remember correctly, if you uncheck the sync contacts box in iTunes, you will be asked if you want all contacts removed from you device.
I have also downloaded an app called ContactsBckp. In the settings of this app (you have to scroll up to see it) there is a remove all contacts option. When you have your contacts all sorted out, this is also a really easy way to keep them backed up.
Another useful app I use to keep my iPhone and iPad contacts the same is called iDrive. You can use this to restore from another device (after deleting all contacts using ContactsBackp).
It may sound complicated, but I have found using these two apps easy and quick, and I have peace of mind knowing I will never have to go through all that mess again.
Hope I have given you something to look at.