Although Brussels is the natural starting point for discovering the little diamond that is Belgium, I advise spending most of your time exploring the Flemish half of the country. The great thing about Belgium is that it is so small, full of treasures, and still a little off the beat in path.
Everyone must experience Bruges. Yes it's touristy, but it is so for a reason. The city is magical. Definitely find a hotel (I stayed at the Botaniek and Nicholas) and spend a night or two. The city might be a little pricey, but the best thing to do in the city is free. Walk around the old side streets at night, gaze at the canals, take in it's medieval glory.
Once you get your full of fairy-tale Bruges, base yourself in Antwerp. It is overlooked by tourists in favor of Brussels, but it is a quirky and vibrant city, and a real center of Flemish culture. Antwerp is home to great jazz, worsterbroodjes (tasty treats), nice architecture, and awesome chocolate. The best food I had in Belgium was in Antwerp.
Daytrips from Bruges and Antwerp are many. Ghent is a wonderful Flemish City. Kind of like Bruges step-sister. There is a resemblance. But while Bruges is polished and almost museum-like, Ghent is down to earth, and has a great lived in feel. The Castle Gravensteen in the middle of the city is spooky like a castle should be. Check out the torture chamber. Ypres is out of the way but it is another lovely town that still honors the fallen of WWI everyday at 8pm in the center of town. Talk about history! Oostende is a great place to relax if it gets hot. The beach is hot, the North Sea freezing... very strange.
Belgium is a great country for the experienced traveller and the new traveler. Great food, history, and english-friendly. Brussels has its share of visitors and they can keep MannenkinPis. Flanders is not to be missed.

those all sound like great ideas. Im going soon and I am going to try and check out your tips. If you have any more please post!!