The user will always have the option to just checkout with PayPal at the top of the checkout page. This should be fine because if the user wishes to pay with their PayPal account then this is the option for them. If they wish to pay by credit card or through one of your other offerings they would choose so from the select list. You should be able to store the information about this selection directly into the table with the store order summary server behavior on the confirm page. Please post back if I'm not understanding the situation correctly.
