It depends on, some of the retails stores will honor the educational discount if you can bring in the current student ID card, not majority of the retail stores will do that though. So you have to call the local stores itself to find out for sure.
Apple retial stores will only have standard configuration machines in stock, any CTO will be done on Apple's site. Staff at store may help you place the order, just like you place the order online. Then Apple build it, ship it to you.
Secondly, if you really need a CTO. Just do it yourself online, and if you have any questions, call 1-800-MY-APPLE. If you call in, and the sales rep spent their time answered you questions, helped you configure a computer. If decide to get it, go ahead place the order ON THE PHONE. These people are just working as hard as you and me, if they helped you, they deserve the credits too.
I have a friend works at Apple Direct sales. He told me there are alot of people call in for questions. After asking 1 zillion questions, then just hang up either order online or go to the store order the same CTO then have it shipped to them. If the sales rep is not helpful is onething, but if someone is willing to spend 20-45 minutes with you on the phone to asnwer all of your questions, if you think you are satisfied with the service, if you think you are treated well, as return, give them the credits they deserve.
To me, people like that just plain suck, no courtisey what's so ever.