Having a car helps a lot. It allows you to stay farther out and get into the city fairly easily. Roads downtown have a confusing grid, so map or GPS are mandatory. Avoid driving in peak rush hours as Seattle traffic is as bad as L.A.'s. If you have Holiday Inn points, this is a good time to use them as hotel prices in Seattle are now at their prime.
I've not seen Bourdain's Seattle, but my approach would be a little different. Bourdain is mostly looking to find places to eat and discuss food. I'm into a day of sites, then towards the end finding a good meal to finish the day. Here's how I'd approach Seattle.
Day 1) Waterfront, including Pike's Market and adjoining shops (including world's first Starbucks). I'd also head down to the Aquarium and Harbor area. This will really take most of a day, especially if you want to linger at the market and people watch. same is true of the waterfront around the Aquarium. End the day by wandering into downtown. Downtown is nice but not unlike many other large city's downtowns. Pike's Market is unique.
Day 2) Need to go up the Space Needle for the view. Best view of the city, but if it's pouring don't bother.. There is an interesting complex of museums and buildings adjoining the Space Needle, including some you might like. Take a look at the architecture of the Sci Fi Museum, even if you don't care enough to go in. There is an interesting glass museum, etc. http://www.seattlecenter.com/ You could spend all day here, but probably a half day is enough
Other options: I am fascinated by flight. The Boeing plant in Everett gives tours of its production line (2 aisle aircraft, probably will now behighlighting the 787). There is also a great plane museum south of downtown, the Museum of Flight. If you share my amazement at the miracle of flight, such a modern invention really, these are fantastic places.
If you've great weather, consider a trip to Mt. Rainer or if you're coming up from Portland a stop at Mt. St. Helen's. These are both lovely natural attractions.
My own blog on this gives more details if you're interested: http://drfumblefinger.com/wrdprs/blog/2012/12/seattle-washington-coffee-capital-of-the-world-and-a-city-of-many-other-nicknames/
Good luck! I think you're ready. Just need to get that room.