The reason that you have two merchant accounts is that you process credit cards in different ways. Some transactions are done with the card present whereas others are not.
If you use the wrong type of merchant account, you will end up paying more in fees. We purposely set up both types of merchant accounts so you will be sure to save the most money by getting the best rate for the TYPE of transaction you're doing.
The MOTO [internet] merchant account allows you to process recurring and one-time transactions with a card left on file (Card-Not-Present transactions).
The RETAIL merchant account allows you to swipe transactions when you have the card present.
The processing rates are different for each of these accounts because the rates are based on what type of card is used and if the card is actually present or not.
Having the two merchant accounts allows you to get the best processing rates depending on how the card is processed.