You connect the shopping cart to the gateway and the gateway connects to the merchant account. It is the only way to do it. You choose which gateway you want to use. CC Cart allows multiple gateways that can be offered together to give more choices to the buyer or use alone.
An example would be to offer Google Checkout and PayPal together to offer more choices. They don't require you to use a merchant account and transfer funds into your personal checking account. These transfers are not automatic and take a few days. They charge a higher percentage rate too. Low volume sales usually take this route to avoid monthly fees.
Another example would be to only use a true gateway service like Authorize.net that automatically deposits funds into your merchant account, which is mandatory (no personal checking accounts). The funds are immediately available. They offer lower percentage rates but charge other monthly or annual fees but it's cheaper if you sell higher volume.
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