How do I give customers the ability to see if there domain is taken and then if its not click the link and put it in the order page.

Wel, two ways... whois scripts with this capability, or registrar software (such as openSRS) that are a bit more advanced. I'd check out OpenSRS.com since it might be a bit more towards what you are looking to do. Do you know how you are going to register the domains already?