Card present transactions can be processed through Authorize.Net, but only if you have your account configured for that type of transaction. Card Present transactions can not be run on the same account as eCommerce transactions.
If you do have a Card Present account and choose to process these transactions, you will need to make sure that you are following the Card Present API, not AIM. While the Card Present API shares much in common with AIM, there are subtle differences that must be followed.
In terms of interacting with card readers, this isn't something that we can really help you with. You will need to review the documentation for the card reader that you purchase in order to learn how to interact with it.
