Is there any way to obtain EPP/Corp pricing via an online purchase through the Mac website? Or would I have to take the purchase in to a local store with the receipt and have them return it and then repurchase it with the discount?
It depends, Apple generally has a specific link for each company where those employees can access a specific version of Apple's online store where you can find the discount. You may be able to chat with a rep to find the one relevant for you.