If the negative terminal on all of the batteries runs to the same ground then there is no way you can get 24 volts from the batteries. The Batteries would need to be wired in series neg to ground, positive to neg on the second batter and positive to to buss to get 24 volts. Make sure your alternator is grounded properly as well. With the switch to both you are using the amperage from both batteries and only 12 volts if the batteries are wired with the negative terminals all grounding. What specific problem are you having?
Ok just reread to find the problem. I'm not sure where your battery switch is in the circuit. With one battery the wire should go from the battery to the solenoid, from the solenoid to the alternator and to the power buss. (there are variations on this but the main power should go to the solenoid, power buss, and from the alternator to one of these points) From the power buss to the ignition switch and from the switch to the coil (x2 Start wire and run wire), and to the solenoid to engage the starter when in the start position. From the solenoid to the starter. (sometimes the coil start wire comes from the solenoid instead) Run position on the switch either powers all the gauges ect. or gives power to a relay that provides that power.
It sounds like either your switch doesn't send power to a single distribution point for the alt, solenoid and battery positive buss, OR you don't have the block grounded properly to the negative terminals of the batteries and is grounding back through when you hook it up. Ground should be both battery negatives to the block, and the negative power buss to the block or negative terminal of one battery. The grounds sharing a common terminal ties all the grounds together so don't worry about switch position.