Depends on your isolator type; for semiconductor type, the SCR/Diode will consume minimum of 0.2 volts drop and varies with the charging current across the blocking device, and thus your battery will never see full charging voltage coming from your alternator. That's how diode work unless manufacturer use more expensive Schottky Diode. This diodes costs more to fabricate than blocking types or SCRs, typically used in electronics device where overall efficiency is critical. Relay type has minimal drop, but these devices typically have short life span.
Your battery is charging as long as your alternator is engaged, although it will never be fully charged. As far as your alternator, it doesn't matter how many batteries are connected or the type of battery used. Alternator will produce constant current and voltage regardless of your load. Your batteries, especially the high capacity one, will take a lot longer to charge. This is another reason why it become less desirable to charge your expensive battery with vehicle's alternator as explained in following paragraph.
All battery charger, regardless of types, will be handled in three distinct charging phase. You want your charger to provide constant current until battery reaches full voltage, then switch to constant voltage mode, give juices as chemical in the batteries stabilizes. Lastly, once battery reaches optimal charging voltage and stabilizes at set point, you don't want to overcharge your batteries, hence your charger needs to operates in tickle charge mode, similar to constant voltage mode. This charging algorithm is used all batteries types; lead type, glass gel or lithium all obeys to one universal algorithm.
Do all battery charger obeys the same rule? NO. Some cheaply made Chinese labeled don't, and it's often difficult to get the correct information from customer service dept, and therefore, insist you want to talk to a real engineer who understand electronics. Everyone wishes to call themselves as an engineer, but not too many people knows their material. It's a reality.
If you have such large capacity battery, it would be prudent to have a dedicated charger for auxiliary battery only, because typically alternator is not designed to produce current needed beyond vehicle's primary battery. You won't need to be concerning with your wiring because your isolator will do what it suppose to do, that is, blocking charging current to vehicle's primary battery. Otherwise, you're going to subject to overcharging vehicle's battery, that will just about obsolete the isolator, but you won't have to worry because isolator will take of it for you.
Some people argue having an isolator charging two separate battery of different volatge is not the right way of charging, creates all kinds of complexity for your vehicles' electronics. Technically, this argument makes sense when you think about it, but not all electronics are made same, some built with higher tolerance to abnormalities.
As far as how deeply you want to discharge your battery, it's your choice. You trade off how long you want your batteries to last vs. how often you want to charge your battery. East Penn Manufacturing, one of the largest battery manufacturer in the US has an excellent resources, technical documents that will excite your brain, showing all kinds of graphs, and their customer service department has one of the most knowledgeable and technically capable staffs I've death with. It's very rare a company will hire technically capable staff for Customer Service group, but this company is different. If you cannot find an answer you're seeking, I suggest you call them, spend hour or more discussing your situation, you'll be educated, in a level you think you're an expertise in complex chemical engineering of batteries.