The wiring would depend on how many banks your battery charger has.
Typically there is one common ground, and frequently two positive leads for two separate banks. Since you have three batteries, that leaves you with the decision of how to rig them. In my case I also had a starter battery, and two group 31s for a house bank - but I kept the house bank connected in parallel with a jumper cable. That way I could lead one positive lead from the charger to the positive lead of the starter battery, and the other to a positive lead of one of the two house banks.
If you don't want to connect your two batteries in parallel all the time (something that Nigel Calder recommends, but many folks do not support) then you would have to choose what to do. At that point you probably would want to hook the second positive lead up to one or the other batteries, or the 1-2 switch itself, and resort to always putting the switch on "Both" to charge them. But I wanted to avoid that, so that's why I rigged things as I did.
If you have a three bank charger, then run one positive lead to each battery. If you have a single bank, then you need to get creative, and have to remember to put the battery switches in the right positions to hook up all batteries to that single lead when charging. Or you could put the two house batteries in parallel, and charge the engine battery with a battery combiner (read about those at West Marine). Endless options.
For sure you don't want the power to run directly to the panel, as you want to be sure to be able to isolate sensitive electronics on those times when you equalize the batteries.
By the way, it is a well understood law of boating that if you ask "n" skippers how to hook up their electrical systems that you will get back at least "n+1" different ways to do it. This same law applies to picking the best anchor.