A standard automotive alternator will not fully charge deep cycle batteries. The best it can do is about 85% to 90% and that's if the batteries are good, all the connections are good, and the alternator acts as it should. There are three stages to charging deep cycle batteries consisting of a bulk charge, an absorption charge, and a float charge. If your charging source can not accomodate all 3-stages (be it an alternator or a charger) then it can not fully charge deep cycle batteries.
The regulators in standard alternators are very simple switches and simply sense voltage; when the battery voltage is at some low point they turn "on" and send current to the batteries, when current is at some high point they turn "off" and stop the flow of current. Think of it as a light switch, it's either on or off. On the other hand multi-stage chargers are like a dimmer switch, not only does it have the on/off function but it can determine "how much" current to send; a stock alternator does NOT do this and always send all the current the alternator can produce to the batteries. Automotive alternators are voltage regulated and not current regulated (other than by maximum alternator output) which means they can not following the charging curve set by the battery manufacturer to fully charge deep cycle batteries. A good multi-stage charger (or 3-stage regulator on the alternator) will current regulate the charging and will bring the batteries back up to 100%. It does this by sensing the voltage of the battery and regulating current flow to the battery based on set points programmed in.
Automotive alternators are designed to charge starting batteries which have many thin plates with a lot of surface area that will quickly absorb the charging current and bring the battery voltage back up quickly. In this scenario the on/off switch operation of the regulator works fine. They are not designed to charge deep cycle batteries which have much thicker plates with a much reduced surface area that takes a comparitively long time to charge. When the simple on/off regulator senses that the voltage of a deep cycle battery is "ok" the battery still has another 15% or so to go before it's 100% charged (beacuse the interior of the thick plates hasn't reconverted) but the regulator doesn't know how to deal with that.
An OEM automotive alternator is not "hot rated"; it can not and should not put out it's rated amps for any length of time or it will die a quick death. You can not expect an alternator that's labeled 120-amps to put out more than perhaps 100-amps or so if you want it to last. If you add enough batteries to your bank to drive the required charging current higher than that you'll damage the alternator.
Charging deep cycle "house" batteries from an automotive alternator that has not been fitted with a 3-stage regulator is a "make do" situation. That is, you're only doing it to get the batteries at least partially charged between times when you can plug in a multi-stage charger. You can get your bus alternator to do the job correctly but it takes a rather expensive 3-stage regulator added to it to make that happen and you need to make sure the alternator is sized appropriately to the battery bank being charged. You can add enough batteries to limit current to any individual battery but you'll exceed the capacity of your alternator's continuous duty rating very quickly. Either way you'll end up replacing something.
I replace deep cycle batteries all the time that an automotive alternator has killed. The problem is that in what should be the the last two stages of charging (when you're trying to reconvert the interior of the plates) the alternator which only has one stage is sending way too much current to those thick plates and they're being damaged. That's specifically why a multi-stage charger is a multi-stage charger, for the life of the batteries the current must be reduced in the absorption and float stages and a standard alternator regulator can not do that. Limit the time you have your house batteries connected to the engine alternator.