Spur of the moment travel. Traveling 6 days with 26 yr old son beginning in Amsterdam and leaving out of Brussels, end of April 2012. Will probably rent a car in AMS to get to Brugge so that we can do some exploring in between. Not sure whether to take train then to Brussels from Brugge or continue driving. We plan on doing a bike tour of both cities as well as Brussels (love those).
Am looking for boutique hotels, not very expensive. Plan on doing the Heineken museum for him. We both are foodies and like to do "locals" stuff.
Any recommendations as to how to break this up in 6 days and also hotel recommendations and "must" sees.

Since you seem to plan to rent the car in the Netherlands and drop it off in Belgium, you should consult the fine print how steep the extra fee for that will be.
Weather permitting, I would find bike tours not IN the cities but to nearby places almost more interesting. Or a combination of a train+bike day trip. Especially in NL with the extensive network of bike paths (often more like bike roads).
Not sure if 6 days is enough for two cities, one town, and lots of exploring going between places.
Personally I would probably "do" 3 nights A'dam, 2 nights Brugge, and one night Bxl, if I was forced to squeeze it all in 6 days.

The drive from Amsterdam to Brugge is not scenic, but motorway and stress. Take the train.
With only 6 days you do not have time for any exploring in between anyway.

I think you are trying to do too much anyway. Day 1 you will be jetlagged and not able to do a lot. Day 2 will be seeing Amsterdam. Day 3 transfer to Brugge, day 4 Brugge, Day 5 Brussels, Day 6 home? When are you fitting in the cycling?
You are aware that 30th April is Queens Day and Amsterdam will be full?
You don't do Amsterdam justice with one full day and maybe 2 half days.

that's what i'll do cowboy!

Did the opposite trek. Flew into Brussels from LAX. I took train from airport and spent the day strolling thru the heart of Brussels. Then jumped on a train to Bruges where I spent two idyllic nights recovering from jetlag; this is a magical place at night. Hotel Prinsenhof was a winner. Lots of cute restaurants for beer, mussels, frites. Looks like a fantastic place for biking and it will be light into the evening. I took the train to Amsterdam where I spent 4 days, the ride was scenic and relaxing; glad I was on train instead of driving. (From A'dam I went to Paris for 8 days. This was a great trip!)

Thank you all. Had to reverse my trip because could not get a hotel in AMS due to tulip showcase, will start in Brussels and somewhat follow vivi.