Upvote:1
Customs are on arrival in San Salvador while going there. Unless you really have a reason to declare something and put anything but Nothing to declare (Nada que delcarar on the Spanish form), this is a trivial matter. An English form is usually given to you on the plane, which you should fill out in advance and hand over after picking your luggage.
When you have your luggage there is a separate lane to leave the baggage area for people that have nothing to declare, just hand in your form and press the button when instructed. If the light turns green, keep going, otherwise it will be red and you will be asked to open your bags so they can be inspected.
Assuming you have a return flight, you will also do customs in Atlanta on the way back.