Not sure about B&Bs in downtown Seattle. It seems your best bet would be a hotel--check out the Edgewater Hotel on Alaskan Way. It is close to all of the mainstream touristy stuff (if you're into that) like Pike Place Market, museums, the aquarium, Argosy sightseeing tours, Ivar's Seafood, etc.
The Icon Grill on 5th Ave is one of my favorite restaurants! Everything I have eaten there has been spectacular and you can't beat the beautiful blown glass environment...it's gorgeous.
My favorite coffeehouse, The Green Bean on Greenwood Ave, might be too far north for your short stay, but they serve Brown & Co. coffee that is by far the BEST I have ever had in this coffee laden area. The original Starbucks is at Pike Place Market, if you're sticking to the mainstream path.
As far as touristy things, I'd definitely steer clear of the Ride the Ducks Tour--obnoxious!
Some off my personal picks:
I've lived here all my life and I still love going to the Seattle Center, home of the Space Needle. The Center House almost always has (free) public events going on. The International Fountain is one of my favorite spots to hang out and people watch.
If you're into parks, don't miss Gasworks Park. The Essential Bakery Cafe on 34th is in walking distance from there. There is also an amazing kite shop on Wallingford Ave if you have time for your inner child
If you appreciate artsy little shopping areas full of unique boutiques and little restaurants, check out the Fremont shopping area. It's just minutes west of Gasworks Park. The Fremont Troll is there as well if you're into that.
If you enjoy asian food and imported goods, don't miss Chinatown/International District. Uwajimaya is one of the best asian markets I can think of. I love to get bubble tea and wander around through all of the shops in the area.
I would drive since you only have a couple days. Our transit system isn't the greatest--you might end up waiting around a lot and be forced to sit next to smelly lunatics for obscene lengths of time
Have fun and let me know if you have any specific questions.