It should be on both while running to charge both, when you stop overnight switch to house bat and cut off engine bat. remember if one bat goes down it will kill the other soon after. Thats why when you change bats you should change both.

http://bluesea.com/viewresource/684

13 volts is def. to low.
The altenator should put out atleast 13.8 volts .
Also i never had a problem with OPTIMA .
And yes each engine should charge 1 batt.

Mike, if you take your Alts off and take them to any of the auto parts stores like Napa, PepBoys, Murrays etc..they can test the alt to make sure its working properly. If you want to rebuild them i suggest MG Auto Electric 500 S Arthur Ave Arlington Hts ..they do some good work and quick turn around. 847-394-1698

Velocity Vector, You should run the switches only on each respective battery for each engine So if the Port side engine is No1 then that switch should only be run on position 1 when running and the same for the other side (alldepends on how the boats rigged) then if you need extra starting juice or have a dead battery switch to the other or to both postion....last thing you need to have one alternator fry out...then overload the other alternator and possibly even fry out the batteries! That link you posted to Blue sea also states:
"Port engine battery is connected to port engine circuit, starboard engine battery is connected to starboard engine circuit, circuits are isolated

Thanks Wally. My boat is rigged kinda weird...the guy that had it just chucked the 502s in it so he could trade up to a 42...I've monkied with the switch settings before, but always just ended up going with "Both" cuz it worked!