There are 3 lines: coffee/sandwiches; deli and pastries (in that order, left to right). Make sure to get in the correct line or you'll have to line up again.
I've eaten at the Nova Era bakeries in Toronto for years. A Yelper mentioned that it was a bit of a culture shock for her there - newbies don't know 'the drill' and people don't help. Same here. Welcome to the world of Portuguese cafés.
I stood in the wrong line for a tosta mista (grilled ham and cheese, then had to line up on the far left. The 4 employees on that side were very busy. The oldest lady who manned the coffee machine near the cash register would shout out, "Next!" I didn't know she meant me so I just stood there and waited for her. Meanwhile, people behind me would shout out their orders over my head! Eventually, I figured out what to do.
After enjoying my sandwich and coffee, I got back in the pastry line (far right) and chose a bunch of the croquettes with 1) codfish with olives and 2) shrimp. Scrumptious. Also got some mini egg tarts for my old lady friends. It's nice that they make the egg tarts in 2 sizes as well as chocolate ones.