As a dedicated boondocker for many years, I've written several times about how to manage generator battery charging. Rather than write more stuff, I copied and pasted from past discussions. I have solar now and rarely have to pull out the generator, so it was better for me to look up old posts.
Couple points that are not in the below posts - make sure your water heater stays on propane. Turn off the AC switch if it is dual heating. Same with your refrigerator - run it on gas only. You want all that charging juice to hit the batteries, not running appliances that are more efficient on gas. Lastly, all I ever did was plug the trailer shore power cord into the generator. I never carried a separate battery charger.
Past posts.
6/2012
Depends on how discharged they are. And the key thing is to not let them discharge any more than necessary. So if you're going to boondock for several days or more, you want to run the generator every single day, starting on the first full day of camp. It is better to keep the batteries topped up, than it is to let them deeply discharge and then try to bring them back. I usually schedule between 1 and 2 hours per day for generator charging. That will keep me up around 90 percent. The last 10 percent takes a very long time to recover, and is an inefficient use of the gen.
6/2012
I've learned that the key to boondocking with battery and generator, is to charge for 1 or 2 hours per day, beginning on the very first day. Don't wait until you need to charge. It is better to keep the batteries topped up than it is to try to bring them back from a deep discharge.
This is also why solar charging works so well, but that is another topic.
It will take a long generator run time to fully recharge batteries. I'm talking 24-48 hours. Not realistic.
9/2011
I've found that in practice, I can get through a week of dry camping very nicely by running the generator between 1 and 2 hours per day. That keeps me in the 90% range. It is that last 10% that takes so much time, and you don't need to try for that. And it is important that you start charging that on the very first day, so the batteries don't ever get too low. It will seem like you don't need to charge on day 1, but it is important that you start replacing the used amps. If you have to run a heater overnight, that really uses the juice and you'll have to extend the genny time. But if you don't have a quality converter or standalone charger, you will fall further behind each day.