I'd put the charger on the chassis batteries, Gary. Usually both the engine and the generator start off them. Then, after many hours of charging, see if the generator will start; it will take less juice to get going than the engine, and you don't want to stress the engine alternator anyway, by forcing it to charge everything that's depleted. That's the generator's job.
Assuming your chassis batteries are each 12 volt, make sure there is plenty of ventilation around the battery banks. If you have a large master switch in the battery compartment, or elsewhere, switch it off.
Clip the positive charger lead (red) to the positive post that has the long heavy positive cable attached on one of your two chassis batteries. Put the charger's negative lead on the battery ground post that has the long heavy ground cable attached to it, or if possible it is preferrable and safest to clip the negative lead to a chassis bolt, away from the battery bank, that has no paint and has been cleaned of any rust and dirt.
You are trying to charge up two batteries with a 6 amp charger; give it lots of time. Then turn your master switch back on and see if the genset will start and help charge up the coach batteries. You might want to invest in a better charger. I got one, for less than $100, at Sears a few years ago that I love, because it is small and easily portable, has multiple charge rates, handles several different types of batteries, can boost start car engines (not big diesels), and monitors the charge condition as it goes with a bright digital readout in either volts or % charged. I've never had to try it on my coach, but one could conceivably try to start the genset with the Sears unit's engine start boost function, as the generator doesn't require as much amperage to start as the engine.
I also benefit from a Battery Minder (Camping World & others), a small, easily stored box that helps keep batteries float charged, and can equalize-charge older batteries with sulfate that needs to be "knocked off" their plates. I usually bring back low automotive batteries with the Sears charger, then use the Battery Minder to recondition them over a couple of weeks. The original battery on my '97 F-150 pickup lasted 12 years that way.
If you go to Sears, pickup a good multimeter as well, so you don't have to rely on your control panel readout entirely. It will come in handy also for checking that campground electric hookups don't have faulty voltage readings before you plug in and burn up an A/C unit or something.
There are a myriad of reasons why batteries get drained, which is a good reason to have and use a master switch for the chassis batteries during storage, and another one for the coach ones as well. Your batteries may be at the end of their lives, and can't hold a charge as long. Others will likely chime in here to offer ideas, as I am not familiar with your specific coach. It may be revealing that both banks of batteries have discharged.
-Joel
