I have been to a little restaurant (not much in the atmosphere dept--just food) in West Seattle on Roxbury Street & 16th(or 17th) called the Salvadorean Bakery (I think?), they have a range of pupusas and more actual food in addition to good baked goods. I know that another place opened a while ago up north on Aurora maybe. I was very happy to find the salvadorean bakery for pupusas because when I moved here from Wash, D.C. it was the food I missed the most. El Toreador (now called Rosita's) on Holman Road used to serve pupusas and other salvadorean fare. There is a place on 1st Ave in Pioneer Square (near Cherry St.) that serves pupusas as well although I have never been there myself. I hope you can find what you are looking for.
Seattle, WA