The “fietsroute” website gives you all kinds of info about cycling routes through Belgium, including Bed&Bike. With the “Cycle Node Networks” you can put your own tour together at home before you start. Each crossing has it’s unique number, signs direct you to the next one, so just follow them as planned. http://www.fietsroute.org/cycling/belgium
I live just north of Ghent and Bruges in the Netherlands and quite familiar with that part of Belgium. The Flemish part of the country is notorious for it’s ribbon development and makes it to my opinion a bit lesser attractive and so harder to find a bit of unspoiled scenery to enjoy. But by planning as much as possible through the countryside you can get the best out of it.
As Belgium has a lot of open flat countryside there can be strong wind to deal with, effective planning can help to avoid headwind as much as possible. Main roads, but not all have dedicated biking lanes (but back roads not), a part are just lanes marked on the road with fast traffic passing by very close. It makes sense to my opinion to have a look with google streetview for an impression how the roads look like.
There are many options to plan a route. I think most of the time attractive, the quickest and also to my opinion the safest are those along the canals between Bruges and Ghent, like “kanaal Gent-Brugge” or more north Schipdonkkanaal between Damme and Deinze. Both canals cross each other some 15km west of Ghent.
Also sections along the Schelde river between Ghent and Antwerp are to consider. Especially “Klein Brabant” the countryside around “Kasteel Marnix de Sainte Altegonde (only visible from the opposite side of the river / Binnendijkstraat) are to my opinion worth to bike through. I am not so familiar with the areas between Brussels and Ghent / Antwerp.
Anyway to recommend is the countryside north-east of Bruges along the canal to Damme and further to Oostkerke and even Sluis and nearby tiny but lovely Sint Anna ter Muiden in the Netherlands. If you have enough time detours through Zeeuws-Vlaanderen in the Netherlands are to consider to my opinion.
Hopefully this can be a bit of help, enjoy your trip!