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In e-commerce, the critical link between the shopping cart and the merchant account is the payment gateway. The gateway takes your customer's information (name, etc.), order information (amount, order number, etc.), and credit card information (account #, exp. date, CVV, etc.) and transmits it all securely to the payment processor for authorization. Depending on the response from your customer's credit card issuing bank and your AVS settings, the gateway will either provide you with an authorization number or a card declined notice. Depending on your cart's settings, your customer may be able to see immediately that their card was approved or declined. There are many payment gateways available, but the majority of e-commerce sites use either Authorize.net or Verisign. Personally, I prefer Authorize.net. I used them for 7 years in my own e-commerce business, and I received better service from them than Verisign. There are more details than I can cover here; I'll give you an address to an article I wrote elsewhere that goes into greater detail:
If you have already gotten your merchant account, and you told your payment processor you were starting an e-commerce business, they should have offered to set up your gateway at the same time. That's typically how it's done. Your processor should also be your best source of information about the proper gateway settings, etc. There are many of us here in the forum who represent payment processors. If you haven't yet set up a merchant account, or if you have more questions, I'd be happy to help. You can find my contact info by clicking my profile to the left. Good luck!