Yes exactly, it is "distributed by demand" .. If one bank does not need it then the other bank gets it. If both banks need it the output gets divided. The total output won't exceed 40A on the entire unit though..But each leg could see 40A at some point. If bank #1 is full and bank #2 needs charging, it will selectively charge bank #2 at 100% capacity. At that point, bank #2 will see 40A.
The fuse for each leg should be at a minimum of 120-150% of the chargers rating. It is better, performance wise, to fuse to the max ampacity of the wire to minimize voltage drop.So make sure that each leg has at least a 40A fuse.
Fuses, circuit breakers etc. should not be run at more than 80% of their rating long term. But still with solar and charging sources you are best to size to the max ampacity of the wire you are protecting as this will minimize voltage drop..I had that problem two years ago when I installed my Truecharge2. I was fused for 30A per bank but was only using one bank at a time through the selector switch. So when I came back to the dock, I would plug in, turn on the charger and blow a fuse.