Hi John,
I guess there are two parts to answer:
1: How much charge is flowing to batteries when towing?
2: Why your batteries ran down when charging with the generator.
To answer Part 1:
From my experience, Jayco just run a small lead from the trailer plug. Usually these only go direct into the 12 volt van system which now-a-days is not sufficient for a number of reasons to keep up with most loads let alone charge the battery or at least keep it floating.
There are a few reason for this.
1. Over the distance from your car battery to your van battery, with a small gauge cable, with the cable being small gauge you limit the current due to the volt drop. So in reality, you might be lucky to get a couple amps.
2. These style of connections do little for battery management and with today's brand new alternators, they are struggling. New alternators drop their output significantly to help with emission control ratings so you are up against the wall.
The answer:
In my opinion, if you want to draw a nice load form your house (Van) battery, you need a decent charger (15-20 amps) and one that is designed for the job, preferably a 3-5 stage charger that will look after your significant battery investment.
Redarc make a couple of nice versions of these. The BCDC 12/20 is a nice compact unit that will do the job and the BMS1215 is the Rolls Royce Battery Management system that allows you to view battery status etc.
The big thing with these pieces of kit is that they will help manage your batteries charge rate depending on its status and also help compensate for inadequate wiring circuits from your car battery to house battery. Ideally you want a nice gauge cable running all the way via Anderson style connection at the car hitch area.
Part 2:
Without knowing your full setup at the time, I suggest that the charger you were using off your generator (I am guessing it was 240Volt charger that outputted 12 volts etc) that is was too small and was only a few amps. Again, maybe enough to keep up with your Waeco but not enough to also recharge it from the night before use.
Just think of it all like water tanks, hoses and pumps. The bigger the pump, the more flow it can push out, the bigger the pipe, the more flow you get due to less resistance and the bigger the tank, the longer it takes to empty it - and fill it..
Ideally, you never want to empty a battery bank more than 50% as it effects their life length, secondly you need to keep them floated (solar usually does this) and thirdly, you want to charge them gently (via a 3-5 stage charger)
One thing that catches a lot of people out is that a 3-5 stage charger will slow the charge rates down a lot during the last 15% odd percent when topping up to 100%. Hence the charge rate is non linear.
If your roughing it and have no battery management systems. Best option is have a Redarc BCDC12/20 (to charger from your car) fitted and a good 240Volt charger to fill it with geneset and then occasionally measure your battery voltage with a meter. The voltage will give a pretty good idea of the state of charge. I fitted the BMS as it Auto switches between Car//240/Sol depending on which is available.
Hope that all makes sense.
cheers
Troy