How to process items after a manual shipping cost quotation?

Hi,

I have some products that require a shipping quote rather than an "add to cart".

Once I give a shipping quote to a customer, how then do I put it back through the store so the customer can use the online interface?

I would rather keep everything in the same system rather than do a manual order via another service, which doesn't look very professional either.

Off the top of my head, all I can think of is to make a new shipping option specific to that customer's quote, but sadly that would be visible to others, and other shipping options would also be visible to the customer in question.

Thanks for any tips