There's a field that settable in the backend for each product called product_url... if you wanted to, you could keep it blank for regular products (ones that will use the regular checkout process), but when you have a custom external checkout required, the flypage could be modified to check if product_url is different not equal to ""...
In this case, the Add to Cart link could be replaced with a different link (perhaps also warning the user that they'll be re-directed to an external link).
--Rich
--Rich