A good place to start is with the handlebars even with the seat, or if that's too low, higher. As you become more comfortable leaning forward you can bend your elbows more, which has the added plus of shock obsorbtion, or ride in the with your hands on the hoods or down in the drops. The important thing is you'll have freedom of choice.
If you start with the handlebars too low you'll spend all your time in one position with your hands on the handlebar tops and your elbows locked and that gets old fast.
If a store is steering you towards bikes that feel uncomfortable it's because they have a stockroom full of I-Want-To-Look-Like-Lance racer-boy bikes with low handlebars and no means of adjusting them upward. Find another store.