Looks like you almost got lost in the rush of things.
Your issue is a semi-common complaint and has some logic to it once we get a bit of experience. Some difference in different RV but this sounds common.
Let me start and maybe act like you know nothing and you ignore things you already knew?? Not meant to insult, just want to be more complete.
Motorhomes have three electrical systems that are only loosely connected. There is the 110 AC from shore power or gen, The coach portion and it works off the coach batteries, then the chassis which works off the start/chassis battery and that is often the parts like a car might have. Where things get confused is that these systems are separated at times and connected other times.
Car starting is pretty much the same on RV EXCEPT that there is often a battery mode solenoid. We have a switch called boost or Aux and we can push it to connect the start and coach batteries together kind of like a temporary jump start. But when we start the engine, that mode solenoid also jumps up to connect them together so that we can get some charge from the engine alternator put into the coach batteries as we move to the next campsite!
BUT that connection is only temporary and drops off when we are not running the engine.
When we are on shore power or generator, there is often a converter which charges the coach batteries, but not the start battery unless we make sure. There are some RV which come with equipment to do both but many do not unless we add something. A very common one is the Trik-L-Start which runs about $50-60 and is easy to install. It connects the two battery strings together so that when the start battery gets down to a certain level like 12.3?? the electronics "borrow" a little from the coach batteries and that keeps both charged while plugged in.
The coach battery disconnect cuts off most but not all the coach stuff like lights, pumps, etc. but the dirty secret is that it still leaves a few things like CO detector, propane alarm, and such still doing a little drain on the coach battery.
On the start battery, there are still things that are draining that battery also. Some are the radio preset, ignition, any auto stuff like door locks, etc. and they will run that battery down over time. How long varies with different RV.
Sounds like you've done it while not using the RV!
So some tricks to learn?
Do open the coach disconnect when not going to be using the RV for a while but it can't fully protect the battery unless you add some form of charging OR actually remove or disconnect one battery cable on the coach batteries.
The same goes for the start battery only there are fewer that have a switch to do the disconnect.
But be aware that letting a battery go flat is hard on them and doing it very often or for very long is going to shorten the life a whole bunch!
Always best when starting the generator or moving slideouts or jacks to have the engine running to make sure to get the best voltage from the alternator! Normal float voltage for the best battery will be around 15. 6, while the alternator will be putting out closer to 14!