There are two parts to configuring your currency settings. The first is whether you want to accept more than one currency and the second is adding the new currency.
Begin by opening your Admin. Point your cursor at Configuration in the top menu, choose My Store from the drop down. If you are running your shop in a language that is not English and are going to use your native currency, click on the line that says "Switch To Default Language Currency" and change the value to true. If you are going to run the cart in English, but not use US Dollars, make sure that the "Switch To Default Language Currency" is set to false.
To add a new currency, point your cursor at Localization on the menu bar, choose Currencies from the drop down. On the page that comes up click the new currency button. Fill in the information appropriate for your currency and check the box if it is to be the default for your shop. Click the insert button, then after the page refreshes, click the update currencies button.