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You can turn off page sync in iBooks.
Whether or not you need multiple accounts depends on you. I set up a 3rd Amazon account just for ebook purchases. It's easier to track that way than having my wife log in to my account, and it's fed by gift cards, so there's no surprises with account balances. And if my in-laws had a Kindle, they could use the account, too, and my wife and her mother wouldn't have to ship paperbacks back and forth to each other. But really getting all of your books from one account is only useful for sharing purposes. If you don't read the same books, it might not matter.
I do try to keep all of our iStore purchases on one account, though, just to make sure we can share e everything. I wasn't aware that you could have two accounts in use on your iPad, and I'm not clear how that would work. When I try to buy anything, it doesn't ask what account I want to use, it just asks for the password to the account I use on the desktop, so I find it easier if everyone just uses the same account.
But I'm also unlikely to buy books on iBooks because the Kindle versions are accessible more places.
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