With 14 days to go, we are fine tuning our itinerary and have decided we can only allocate 1 day to see Bruges and/or Gent on a Monday. We would really like to see both. We would like to just walk around and soak up the ambience of each town and have lunch or dinner in each town. We definitely plan on a canal boat tour and have heard that Bruges canals are more picturesque. Opinions on the which town to take a canal tour to take would be appreciated. Also, which town is better to stay late in? We don't mean a party or bar scene but for dinner choices. We are staying in Brussels so will need to take that into consideration as well.
The most flexible way would be to take an early morning train to Brugge (travel time around 1 hr). Do the things you want to do, including a canal boat trip. Take an afternoon train back to Brussels. If it hasn't got too late in Brugge, you can get off in Gent (Sint-Pieters is the main station; Dampoort is closer to the centre, but involves a change at Sint-Pieters). You won't have problems finding a restaurant. Take the train back to Brussels, which run every 15 mins or so until around 22:00. You can do it all on a return ticket to Brugge.
I would not do both. Decide on one town and do it right. The canals are more beautiful in Bruges, so if a canal cruise is on your bucket list, go to Bruges. There are plenty of great restaurants, and if you like beer, the De Halve Maan brewery tour is really fun--and you can book your tour in advance to make sure you get in.
Think a bit like Ton suggests, so go to Brugge till you have seen enough there and if there is time left you can visit Gent. Best is just going to Gent Sint-Pieters railwaystation and take one of the frequent trams (line 1) to the centre with direction Wondelgem or Evergem and get out at Korenmarkt. Trams (line 1 direction Expo) back run till about midnight, ask the driver or look at the timetable at the platform. Oneway ticket costs €3 per person. From Dampoort you have to walk or take a bus and you won’t gain much if you ask me.