This system will use the solar panel and the wind generator to charge two 12 volt batteries that will power the trawl motor and the starter of the main motor. The system will have a built in switching mechanism that will automatically sense the state of the batteries, in which case it will switch the load from the lowest charged battery to the highest charged battery, then proceed to charge the discharged battery. Ideas or suggested are very much welcome

 

You can use comparator ICs to detect which battery has reached the minimum allowable discharge voltage and switch to the other battery which is assumed charged as not to cause damage to the discharged battery. When you switch the load tho the charged battery you will switch the charger to the uncharged battery to charge it. Another option is to make your circuit not to switch to the other battery (from uncharged to charged) until the assumed charged battery is fully charged. With comparators and a few relays you will make the job but a microcontroller would be the best, less cost and less complicated circuit.