Our SM#160 bow thruster draws about 485 Amps when it is running.  The exact power calculation is complicated because the voltage is not steady at 24 volts, but drops quickly, and significantly, under this load.  The reason the wire looks undersized by standard calculations is that it operates on a very short duty cycle, so heating of the wire is minimal.  If you were to try to push 500 Amps through that wire for an hour, you'd have a real problem.  

At least on our boat, the "bow thruster" cable carries all the 24V power to everything forward of the forward saloon bulkhead.  Mast and genoa furlers, cabin lights, nav lights, windlass...

We have fused our battery bank in two different ways, and both worked well. Keep in mind we have a bank of 4 pairs of batteries, smaller than yours which I believe is 6 pairs.  

Our batteries were first fused with four 125 Amp rated battery terminal fuses, one on each 24V positive, for a total of 500 Amps.  With 6 pairs of batteries you'd end up in the about same place with 80 or 90 Amp rated fuses.  When we changed battery brands, the terminal fuse holders no longer fit under the battery box lid, so we switched to a singe 500 AMP ANL-style fuse.  Never have any of these tripped.

We have also reworked the whole 24 volt distribution system so EACH of the wires leaving the battery box has a fuse appropriate to its ampacity, and the switches now interrupt current to everything except the bilge pump circuit.  To me this is a really basic safety issue.  If there was ever to be an electrical fire on the boat, or a piece of runaway equipment, I need to know I can shut off the power to everything without delay.

On the boats I have seen, Amel was very inconsistent about what wires they connected to which side of the main switches. On our boat, only the battery charger, bilge pump, and "always on 12V converter" were connected to the unswitched side. I think on later boats they just ran out of space on the stud on the switched side, so were forced to move wires to the unswitched post. 

Bill Kinney
SM#160, Harmonie
Annapolis, MD