If you already have shipping rules in place, you don't need to set them up in the wizard. Don't set anything on the shipping tab of the wizard, and it will use your existing rules.
PayPal standard is no longer supported in eCart. Instead you should Express Checkout, this offers the same experience as PayPal standard, it is still a free option, but is a real time checkout system unlike PayPal standard which relied IPN to notify of the transaction status.