The only answers I have are more questions.
Has someone changed the factory wiring? Your post suggests that.
Let us know that and then we can discuss your questions.
On the off chance there is simply a misunderstanding of the standard setup in our tugs.
1. Think of the four batteries as made up of two pairs.
The right hand pair (towards the bow) are the house batteries.
The left hand pair (towards the stern) are the engine battery and the thruster battery respectively.
The thruster battery is the outboard one and the engine battery is the inboard one.
2. The set is not electrically one big battery UNLESS the combiner switch is turned on.
The combiner switch is one of three switches just inside of the opening to the quarter berth (cave)
2A The top two switches are for controlling DC power throughout the boat.
Straight up and down is OFF.
Rotated clockwise one click (horizontal) is ON
2B The single switch below the top two is the Combiner switch.
Straight up and down is OFF (batteries not combined into one)
Snapped one click clockwise (horizontal) is COMBINED (all batteries connected in parallel)
Most of us do not leave the combiner switch set to ON so that if the house set is drained we still have a hot battery for starting the engine.
3. So, if your engine start battery is down but the house/thruster set has some juice left, turning the combiner switch to ON will give you cranking power. I have used it that way twice when starting the engine in very cold weather and the engine battery by itself would not crank the engine fast enough.
4. And finally to answer your question. If the engine start battery is run down and you want to jump start the engine, turn all three switches to OFF. Then put the jumper cables on the engine battery only.
5. And lastly there is a switch for the thrusters. It is half buried under the floor of the cockpit. Open the port side storage locker, get down on your knees and look for it under your left knee. (on my 2009 R25)
Your boat bieng an SC all bets are off but I expect the basics to be similar.