In answer to your question, a merchant account works a little bit differently than a 3rd party processing account.
To start with - you get paid much faster and there are usually no reserves unless there are particularly high risks or issues present on your account.
In addition, you have only your own DBA and phone # listed on the credit card descriptor. This is beneficial both from a marketing standpoint (to show credibility) as well as on the customer service side to make it easy for a cardholder to contact you.
You also have your choice of whatever payment gateway and/or billing software you want to use. For instance, if you use Authorize.Net - you could easily work with WHMAutopilot.
When selecting a merchant provider, depending on your volume - you will want to ask about many common fees such as Monthly Minimums, Statement and/or Support Fees, Gateway Fees, Annual Fees and Cancellation Fees.
If your volume is < $1,000/month on credit cards, it is best to get a merchant account without a Monthly Minimum to avoid paying $20-25/month in extra cost -above and beyond- the monthly statement & gateway fees.
If your volume is > $1,000/month, you will want to get specific % figures on how many sales are downgraded to mid and non-qualified and what specifically determines this. You will find that sometimes a provider with a lower % discount rate will actually make it up by having more expensive downgrade fees which can really add up.
Lastly, if you can avoid a cancellation/termination fee of any kind - that is a plus since you won't be locked into an agreement and have to pay $250+ if you ever switch.
Best of luck with your search!