Definitely go to see the Grand Place, both in daylight and at night. There are a lot of restaurants there with outdoor seating that have decent, albeit expensive, food.
We did the hop on hop off tour one day just to see the city, and because it took us out to Atomium. Atomium's worth a look and some cool photos, but I wouldn't pay to go up in it. It's not worth the cost. Neither is Mini Europe which is right next to Atomium.
Delirium Village has, I think, 6 bars with tons of beers. It's neat just to see all the beers they serve and their glasses. One of the Deliriums is a Trappist bar and that was pretty neat to learn about the history of the beer. Delirium Cafe has over 2000 beers, but is really touristy. Little Delirium was a good atmosphere.
Most of what we did in Brussels was just wander, eat and drink. I'm pretty sure I ate my weight in waffles, chocolate and fries, and drank even more.
For a meal, I really enjoyed La Maison des Crepes which was a tiny restaurant near to the Bourse.
As for sights, I would definitely skip the Atomium (we went up as my h wanted to but what a lackluster attraction). I would recommend visiting the Comic Strip Museum, St. Michael's Cathedral is worth a stop in (stunning stained glass windows) and the BELvue Museum which chronicles the country's history. I'm a history nerd so I really enjoyed it but overall you learn a lot.