How does the result of Request for Freight get paid?

When the customer clicks "Request for Quote". Doesn't it effectively abort the checkout procedure? When I send him the actual freight quote, how does the customer input that amount and pay for it?

Can anyone help on this matter? It continues to be a thorn for me. Customers just don't seem to know what to do. I have "edit order" installed. I have "request for quote" installed. I can go in and change the order to show the actual shipping quote. Can't customers simply go back to your shopping cart and finish checking out with the modified to include shipping cost and enter payment mode? In my last situation, the customer had already checked out with the payment and now I modified order to include shipping and he's already checked out? He went back into his shopping cart and thought he had re-checked out. But nothing actually happened to modify the amount of payment.

Any one with suggestions here? Thank you.

Larry
Alternative Energy Discount House