the Only time to use Both is when desperately trying to start because it won't start on 1 or 2. NEVER leave it on Both.
When on Both, a bad battery will drain the good battery in short order. On Both, you effectively have one battery and when its dead you are screwed.
I will never understand why Dealer's don't install the Aux charging cable on motor and then both batterries will charge independently, all the time, no switching.
The alternative to the Aux charging cable is a VSR/ACR charging relay.
Look into that because having to remember to switch batteries is STUPID.
Skunk Boat has this nailed down correctly. I'm not sure why there is so much confusion and misinformation on this topic. It really is simple.
Your motors have alternators that will charge their respective starting batteries. If your boat has a house battery (third battery) one of the motors has a charging shunt that will charge the house battery too. If you have a fourth battery the other engine needs to have a charging shunt installed that will charge the fourth battery too.
Each motor should be set to its own battery ie port battery to port engine. You should only use the "both" position if one of your batteries is failing to jump start the motor or just use the switches and put it on the other battery. The "both" position is a bad idea especially if you are connecting (paralling) a good battery to a bad battery via the switch. You should never run in the both position.
As far as batteries I'm using all Duracell AGM's purchased at Sam's Club.
Group 34 43.10 lbs. 955 MCA 55 AH. $119.32
Group 24 52.40 lbs. 800 MCA 78 AH. Did not see availability at my store.
Group 27 61.55 lbs. 900 MCA 92 AH. $158.88
Group 31 67.35 lbs. 1,000 MCA 105 AH. $179.74
I used a Group 34M Duracell Marine AGM for my Yamaha F150's. About 9 lbs lighter than a Group 24 and 17 lbs lighter than a Group 27 with higher MCA rating but less capacity. Also used for my 4th battery, a Group 34M Duracell Marine AGM, for bow thruster, windlass and bait tank pumps.
For the house I use a single Group 27 AGM. You could parallel two new ones. Or do a Group 31. I don't like parallel battery setups but if you do this they must both be new and replaced together later on. Mixing confuses the charger and possible battery explosion risk.
Both engines wired with charging shunts. One connected to house the other to the 4th battery. When underway all 4 batteries are charging.