Arriving in Marseille and would like to travel to Paris and then on to Belgium using a rail pass in June. Any ideas on an itinerary that might keep us away from the overly crowded tourist areas but give a good feel for France (and Belgium). Suggestions for overnight stays?
You need to rent a car to visit those kind of tourist areas. The individual guide books on France and Belgium will give you some ideas about where you would be interested in going.
You really need to get hold of a comprehensive guide book to France and read about the towns and cities that are more or less along your route. I'll make two suggestions for places in eastern France that get very few American tourists:
Troyes. It has lots of half-timbered buildings and is great for just wandering around. You won't encounter too many English-speaking tourists, though it is certainly not unknown to the French.
Nancy. It's a larger city known for Art Nouveau architecture (very good small museum). Again, a very good place just to wander and soak up the atmosphere.
One thing to keep in mind is that a lot of the French rail lines radiate from Paris, so it is not always possible to move quickly between provincial cities (even major ones) without traveling into Paris and out again. That takes time and runs up your cost. Sometimes it means you must hop on the Metro to change train stations, which is completely doable but a pain when you're just trying to get from--say--Alsace to Normandy. For this reason, it might be best to pick just one or two areas on the way north and visit multiple towns in each area, thereby avoiding repeated trips in and out of Paris.
If you already have an idea or two of places you might like to see, tell us what they are. We may be able to suggest additional nearby spots worth of visits.