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It never hurts to get a rep, as they may be able to show you things about the machine you may not have known, and if they are well trained, they can answer all your questions and make you feel more comfortable about your purchase.
For custom configurations that are not listed in the store online by default, you will likely need to go online, though some stores have a fully featured configuration with the maximum custom addons all prebundled. For more customization online is better.
Ordering over the phone to the brick and morter store is not as likely to be doable, though some stores may offer it. Each store has their own policy, and I suggest calling them ahead to find out what it is.
You can at least for
http://www.apple.com/retail/ set a genius bar appointment ahead of time, to discuss your needs.