Suzanne, it would be useful if you said that you are flying in and out of Amsterdam, instead, for example, flying into Amsterdam and home from Brussels? What month of the year? Haarlem is a trivial commuter trip from Amsterdam. Our host Rick often urges Amsterdam visitors to stay in Haarlem instead, because it is less touristy and is easy to get to Amsterdam every day for sightseeing. (I don't happen to agree with him. And I think Antwerp is much more attractive than Haarlem, just for example. Of course Antwerp is not a suitable place from which to visit Amsterdam daily.)
Bruges and Amsterdam are connected by train, but they are not in the same country and are not on the same train line. So at least one change is needed. Note that "best" is a vague term. Do you mean "cheapest", "fastest", "most comfortable", or what?
Have you used Google Maps to look at your itinerary? (It's not a good train planning map, but it makes distances and relationships clear.) Please do read our host's general train hints, blue menu top left. You'll be glad you did. Train tickets are always best bought from a national rail company. Are you comfortable with non-changeable, non-refundable train tickets?
Your route is often asked about here. Many people are confused by the fact that Belgian Rail has several trains AN HOUR from Brussels or Antwerp to Bruges, and they do not cost less in advance, nor do they require seat reservations. The long distance trip, which can be either to Brussels or Antwerp, is much chaper bought in advance. Because their ticket onward to Bruges is not for a specific train, you can take time to visit Grand Place in Brussels if your luggage is not too burdensome.