You would need to run the checkout wizard twice, the first time, set the gateway to paypal Pro, the second time, set the gateway to none.
The second time through, set the last step to use unique names for the checkout pages.
After running the checkout wizard, edit the orders table that it creates to add a new column to mark the order as paypal or pay later.
On the confirm pages for each payment method, edit the Store Order Summary server behavior, and enter a value for the payment type (paypal or later) column.
you will also need to add the links to the checkout process for the customer to make there paypal or later selection.