From what you have described.... the charging system goes through the ammeter... to answer your second question... yes... if the battery switches are on "both" the charging systems are connected... along with the power to all the accessories... and the batteries.

Is this ok or should I only use "both" for starting only then switch each battery to that motor.

I prefer to start on each battery.. port on #1... starboard on #2.... Both if the batteries are low... but I have always switched them to seperate batteries while running... my boat was wired with the port charging system powering the port accessories... trim motors etc... and the starboard charging system to the starboard accessories and the cabin power... that way I could run the starboard battery dead while beached... with the port battery in the "off" position... that way I always had one charged battery to start the motors. But... you have to make sure that there aren't any wires connecting the two systems... or both batteries will go dead.

Thanks Reed

I hope that helps.... I has so many wiring problems on my boat... I tore out all the wiring and rewired it... talk about a big job... but everything worked... never had any electrical issues... The previous owner had twisted wires together and then wrapped them with duct tape.... talk about a gremlin breeding ground........:D