In an ideal world you wouldn't mix FLAs and AGMs much less Gels and you wouldn't mix old and new batteries of the same type. In practice I have found it doesn't really matter except for Gels which have quite different charging parameters.
You should set your shore power charger whether it has 1, 2 or 3 outputs to the parameters that the manufacturer recommends for the largest bank, presumably the house bank. Why? Well it is cheaper to replace just one starting battery than multiple house batteries if the slight difference in charging parameters harmed it any.
But it won't happen. Also for most shore power chargers the 2 and 3 outputs get exactly the same charging parameters that the 1 gets. You can't set them differently. So you compromise.
The same is true of the engine alternator which is often hooked up to the starting battery. 95% of the time it is a fixed voltage internal regulator set at about 14 volts that isn't optimum for any battery type. So you just live with it. If it does have an external regulator and you spend lots of your time cruising to your next destination, then I would probably set it for the house bank rather than the starting battery which it almost always is hooked to. Same reason as above. When the combiner/ACR/1,2,all switch kicks in, start and house are all tied together.
Batteries on boats are a compromise and so are charging voltages, but it rarely matters much.
David