The current from the alternator will go to both batteries, since the ACR combines the two banks. However, the house bank, being at a lower charge level would have a much lower internal resistance, so the bulk of the current would end up going to the house bank. As the house batteries charge, the internal resistance will increase, as will the voltage the batteries are at.
As to voltage levels... that really depends more on the voltage regulation system you have installed and what kind of charger you have. Ideally, the charging source should be connected to the side that has the greater load, generally the house battery bank. Yes, both banks will be charging at the same voltage level.
However, to prevent a dead battery bank—not low, but dead—from depleting the other battery bank, the ACR will NOT combine the banks if one bank shows a voltage of less than 10.8 VDC. Given that a 12VDC battery system at 0% charge is 11.4-11.6 VDC or so, this is a pretty reasonable limitation.
Yes, in theory, you could discharge the starting bank into the house bank, but it would require you to be doing some unusual things. Like starting the engine, running it for a very short time period and then shutting it off repeatedly with the house bank nearly dead. If you did manage to run your house bank down to say 11.0 VDC, it would become a drain on the starting battery whenever the battery combiner kicked in. If you then decided it was smart to start and stop your engine repeatedly under these conditions, you'd basically get what you deserve IMHO.
However, in most cases, that kind of idiotic behavior is going to kill the starting battery to begin with, and it certainly isn't good for the engine either.
BTW, since you're generally not supposed to run batteries down much below 50% on a properly designed DC electrical system, the scenario you're describing is one that shouldn't occur except in unusual circumstances. If you find you're constantly running the house battery bank down to less than 12.0 VDC, you really need to either lower your usage or increase your house battery bank size.
This is where I get confused about what, exactly, the ACR does. Let's say the house bank is nearly dead. The starting battery, on the other hand, is fully charged. You start up the engine. So far so good. Now what does it do?
The starting battery has only had a small amount of energy drawn from it and only needs a bit of charging. The house bank, on the other hand, is near dead and needs a lot of charging. A fairly high charging voltage is needed for the house bank at this time, but only a pretty low one for the starting battery. Do they both get the same voltage? Does the ACR actually combine both so that the starting battery discharges into the house bank? And then they both get charged back up together?
What if, for some reason, you only want to motor for a short while at this point, and would rather charge your house bank later? If the starting battery has been discharged into the house bank, unless you run long enough to fully charge everything, then you may have trouble starting the next time!
If you're going to be stupid about the way you use your boat, no piece of equipment in the world is going to be able to prevent you from killing your batteries.
Is this right? Or am I missing something?