[Al Skierkiewicz]

Neat,
The breakers are meant to protect the wiring from catastrophic failure. The breakers are sized according to the minimum wire they are used with. A speed controller wired with #18 wire can be fed from a 20 amp breaker. Likewise, a 20 amp breaker could also be used with #10 wire. It is the minimum wire size that must be satisfied.
I would recommend you use the smaller breakers for smaller motors. Smaller Banebots, window motors and some of the AndyMark motors would fit into this category. Save the 40 amp slots for the motors that will be doing the most work like the CIMs in your drivetrain.