It is very likely that Thalys has a change in Brussels Midi, but I haven't used it for this routing. Of course there are slower and cheaper trains from Brussels to Amsterdam if the Thalys price is not to your liking. I may be confusing Thalys with Eurostar, but see if Thalys has a product called "Any Belgian Station", which might be useful to you. In any case, the local trains from Bruges to all three Brussels stations do not require or offer reservations. They run several times an hour. They can be crowded, especially at rush hour and school rush hours. Sometimes I've had to stand.
I would make my sleeping decision on price, availability, and distance from the hotel to the rail station. Also note that the Mystic Lamb in Gent is open seven days, while few other things are open seven days anwhere. Monday is an important day to check for closings.
Because August is a vacation month in Europe both towns will be crowded, but especially Bruges. (Gent is a bit of a college town, which Bruges is not so much. That also makes Gent cheaper.) Some people post here that seeing Bruges after the daytrippers have left was important to them. I settled for two separate daytrips from Antwerp, because I used to go to Antwerp a lot. It's partly a matter of travel style. I like Gent, but it is perhaps only 60% as picturesque as Bruges. OPINION.