Normally, the coach batteries are charged by the alternator as the vehicle engine is running. If the batteries are not charging, something is preventing sufficient voltage from reaching the batteries. You should be able to locate the problem using a volt meter (or multi-meter).
First, measure the chassis battery voltage while the engine is running. A typical voltage there would be 13.7 to 14.1 volts. It must be higher than 13.2 volts for the battery isolator to allow any voltage to the coach batteries. If this voltage is low a mechanic might assume the alternator is failing, however a bad connection between the alternator and chassis battery may really be the problem. Measure the voltage at the alternator being careful of the moving belts or fan blades. If the voltage is good at the alternator but not at the chassis battery, replace the cable or fix the bad connection. If the voltage is low at the alternator, check that the belt is not slipping. Otherwise, it maybe time for a new alternator.
Once you know the chassis voltage is good, check the voltage at the coach batteries also while the engine is running. If this voltage is the same as the chassis voltage but the coach batteries do not charge, make sure the battery connections are good by disconnecting coach batteries, cleaning the posts and connectors, and reconnecting. Obviously, DO NOT LET THE CABLES SHORT WITH EACH OTHER. If the connections are good, you probably need new batteries.
However, if the chassis voltage is not seen at the coach batteries, you need to check the battery isolator (separator) next. Coach House usually mounts your battery isolator under one of the cab seats. The battery isolator passes the voltage from the chassis battery to the coach batteries only if the chassis voltage is above 13.2 volts. This prevents the chassis batteries from being drained when the alternator is not producing at least 13.2 volts. If the isolator fails to pass a chassis voltage above 13.2 volts, it needs to be replaced.
If the isolator is passing the chassis voltage as it should, you need to check the large amperage (100 Amp) fuse that may be found mounted under the chassis near the battery compartment. Replace the fuse if the chassis voltage is only seen on one side. Replace the fuse and its mount if road salt build up may be conducting to chassis ground.
This post is based on my experience with our 2008 model 241 but I expect it to be very similar for any Coach House Ford chassis.