It depends on what you plan to grow euge, I do mine parallel to the sun so I can grow tall stuff in the back and short stuff in the front. Then again, at only 3' wide you might not really have a front/back, so it might not matter too much. I would only put two pepper plants in a 6'x3' bed, maybe 4 if they were a compact variety. And those beds are small enough that you don't need to worry about prevailing winds and air circulation as long as you don't plant too densely.
Bottom line, I think you're ok either way, but we'll see what other people say.