battery charging hundred series-hope someone can help

What model/engine is your 100series?

1998 diesel standard

"if the isolating switch from the starting battery is turned on will the charge then be directed to the deep cycle battery whilst the car is running?"

Short answer is yes they will charge in parallel, equally if the switch is left in the on position both batteries will discharge in parallel.

(If I've understood your description correctly)

"the starting battery also has an isolating switch off the negative terminal."

Don't ever start the engine then turn both isolators to the off positions as you'll almost certainly fry the alternator. They require the battery as a load to regulate the voltage.

Would I be safe in assuming you bought the vehicle with this setup already installed?

Geoff

Its a very cheap way to isolate batteries, but works fine if you understand the limitations.

Ideally your batteries should be identical in type, size, age and brand, because most of the time (including when you're stopped) they will be connected.

I don't know why there are 2 switches. The switch on the neg terminal of the starting battery sounds useless, so I'd remove it.

If through some fault neither battery is connected to the Alternator, it will produce a massive voltage surge that can destroy the Alternator and the loads.

Once the main battery is charged (and left connected), the Deep cycle will charge exactly as fast as if the Main battery were disconnected - just no danger of catastrophe.

Alternators CANNOT sense the state of charge of any connected battery.

I would remove the Isolating Switch in the Main Batt negative - no advantages - just high risk. If you want to ensure that it doesn't accidentally discharge, put the switch between battery and loads (ensuring the Alternator is always connected to the Main battery)