Charging system can charge multiple batteries, but if alt. is only putting out so many amps, it will take forever to charge them. You would need to upgrade the alt. to one that puts out more amps and then motor will have to run for long periods of time to recharge depending on how much they were discharged.
If you are considering a Microwave, consider a generator instead of adding the weight of batteries. Both Honda and Yamaha both make some awesome little units.
Do a search on this site about use and wiring up a little gen set.
I use a Honda EU2000i, and love it. Powers TV, 5000 btu A/C, microwave, charges house batteries, fridge, water heater, ect.... Of course not all of them at the same time. The EU2000 puts out 1600 watts continuous, 2000 watts peak. Both Manufactures make a smaller 1000watt unit that is perfect for charging batteries and running a small microwave.
I have wired a plug in outlet on the swim deck next to where I strap gen set down. This way I dont have to string cord around to shore power outlet mid-ship.
When beach camping, I put gen set on beach and run 100' cord to boat, can run A/C all night long!!!!! those 90+ deg F nights are no problem any more!!!!
This spring I am going to install a larger HDTV and inverter to power it since it is a 110v vs 12v.
What you need to do is add up all your power requirements, figure out how many amp hours you will use on a given trip. Will a couple batteries support your needs, I would not count on the boats charging system to recharge house batteries unless you motor many hours during the day.
Happy boating/camping
Let us know what you decide