Just to add a 25 cent comment or two to this situation. It is important for new RV owners to learn their various electrical systems and how they “should” operate. The industry (most Dealers) generally seem to do a poor job of educating buyers, new to RV-ing, on how their various coach systems operate, or even where some of the most important basic items are located. The best tool any RV owner should have and learn how to use, is a basic inexpensive Multimeter (measures voltage, resistance and amperage). There are lots of simple tutorials on Utube on how to use them. By the way, it is not unusual for new or newer coaches to have bad batteries.
The chassis battery is used to start the engine and sits in the engine bay typically. Coach or House batteries (typically a pair or more) are used to power the DC loads in the coach (lights, fans, water pump, slides, generator starter motor; hydraulic pump motor for levelers, inverter etc.). As Bob advised, in order to charge any batteries via the converter output (120VAC to 14VDC) the use/store switch must be turned on if you are using shore power or the generator. On many coaches (not all) when the coach batteries are being charged via the converter, the chassis battery may also be automatically connected (based on time and voltage levels) to the coach batteries charging circuit. Similarly, when you are running the engine, the alternator is charging the chassis battery; and in many coaches (not all) the coach batteries can also be automatically connected into the alternator charging circuit. The easiest way to know when (or if) this “charging” is working correctly is to use the multimeter (measure voltage across the + and – battery terminals on chassis and coach batteries). Normal charging voltage is typically approx 13 VDC or higher depending on converter charge mode; or if the alternator is being used as the charge source.
The clicking noise you hear “might be” the relay that connects your chassis and coach battery charging systems together, but without more information about what charge control system you have and the charging situation at that time, it is hard to specify what the clicking is from. Do your basic charge system tests first and find out what is working and what is not, then start figuring out why it’s not working. We learn the most about our coaches when something does not work as it should and we have to roll up the sleeves to find out why. The forum helps along the way too. Happy travels.