What is the problem you're having? A merchant account alone won't do anything as far as your website goes, unless you also have a gateway service (Authorize.net, EPN, etc...). Otherwise, you'd have to manually process everything through your terminal, phone, or whatever setup you have.
If you just mean problems choosing, then it's really best just to compare as many as you can and pick what's right based on your needs & sales volume.
Things to watch for would be any hidden fees, setup/cancellation fees, etc...
Some will have a monthly minimum, some won't. Rates will vary, as will transaction fees, address verification fees, statement fees, gateway fees.
One tip if you're shopping around would be to check out the E-commerce forum section over at webhostingtalk.com. Some of the reps from companies post there (CDGCommerce, Corey Bryant, etc...) and will often have WHT specials in their sig that will get you a discount. If nothing else, searching there should make you aware of some of the ones to avoid.
Also, some companies like Sam's Club offer their members merchant accounts at low rates. Even if you're not a member, if the prices are right, it might be worth the $30 - $50/year to join.
If you're not doing much volume, you might be better off for now just using PayPal, Google Checkout, or some third-party processing company.
The 3rd party companies often charge higher % of the sale, but without the other monthly fees that come with a merchant account. But once you get up there in volume, those fees work out to be a lot less than a jacked-up transaction fee.
No matter which way you go, be sure to fully read and understand the terms on anything you sign. You'll also want to make sure your site meets any security requirements they have, as well as how you handle customer info (use SSL, no storing CVV codes, etc...).