Now that we know you have a non-trojan battery then the boost charge requirement mode drops back to 14.4VDC.
What you learn from from all of this is using a 50AMP charger or even a 200AMP charger your two batteries will only pull around 40 AMPS from the very large charger if you hit the two two batteries with 14.4VDC.
This will charge your two batteries that have been discharged down to 10.5VDC back up to 90% state of charge (around resting 12.5-6VDC) and will do this is a quick three hour charge time. i.e. you only really need a 40AMP smart mode charger setup. Any charger that puts out more than 40AMPS is just wasting your money as the extra AMPS will not be demand by your two batteries. If you purchase a SMART MODE 40AMP Portable battery charger than you can connect that directly to your two batteries terminals in parallel and do the same thing. Hit them with 14.4VDC and the two batteries will demand up to 40AMP of Charge current and will complete its 90% charge state in about three hours time.
Now if you add more batteries later on like maybe two more 12VDC batteries then your smart mode converter/charger unit will need to be increase 80AMPS if you want the four batteries to get charged up to the 90% charge state in a three h our time span. My PD9260C only has 60AMP of DC CHARGE Current available so it fits my THREE 12VDC Batteries in my battery bank just fine. I can charge them back to 90% in a three hour generator run time. I originally had four 12VDC batteries and it would take a bit longer to get them back up to the 90% charge state. added about another hour to generator run time.
The PD9245 or PD4645 converter/charger is all you need for your two 12VDC batteries. Your Honda EU1000i generator will run those converter/chargers just fine by connecting your Trailer 30AMP Shore Power cable directly to the 1KW HONDA 120VAC receptacle using a RV30A-15A long dogbone type adapter from WALMART. You may have to make sure some of the other high wattage appliances are turned OFF when you are doing this. Only have the converter/charger circuit breaker ON is what I do here.
This is what most of us guys camping off the power do with our generator.
Some where down this thread and all those before this a light should turn on sooner or later... This is basic battery science at work here and not much you can do with your different schemes and ideas will change much of anything for the end result.
Roy Ken