Both batteries should get a full charge. The alternator is set by its regulator at a certain voltage (14.4 in bulk) and the batteries will accept what they need.
The problem with charging through the 1,2,both switch is that you have to control it. You have to be in "both" to charge both. If you forget and leave it that way you will drain both.
The advantage of an Echo Charge as mentioned by Bill is the charging becomes automatic. The charge current does not go through the switch and you never have to put the switch in the both position.
An Echo Charge is more than adequate and is less expensive than the DuoCharge.
Living aboard in Victoria Harbour