I figured out how to get around the problem of sending two emails with PayPal. The solution is:
Create a new predicate
Set the trigger to a payment gets entered for an order.
Then make the new predicate an exact copy Email costumer checkout notification
Do the same thing for Email admin checkout notification
Then under trigger costumer completes checkout disable email admin, email costumer and update order status upon checkout completion with full payment.
By doing this Ubercart should only send one email when using paypal website payments standard.