I assume that the generator charges the battery via the charging section of an inverter ( I assume a SW5548 is an inverter)
The Mx60 can be set to a lowish float voltage, assuming that the inverter chargers are also regulated then they can be set slightly higher. The C40 should have the highest setting and it should only dump the hydro.
If your engine driven battery charger can not be regulated then you will have to watch the volts don't rise excessively with the engine running ( bit of equalising)
As Dan said, you would normally not want to run the generator with fully charged batteries. If you have to do so then either switch a decent load on or use a voltage sensing relay to do it automatically as Dan suggests.
As long as the load resistor fitted to the C40 can't take more than 40A you will not hurt it.
Flux