I have a boat, it too has a bow thruster, but it doesnt pull 600a, its 1.5 hp, so more like 90a, it generates a fair bit of noise too.
The thruster is up front while the engine which has an attached 240v ac genset powers 240vac chargers fore and aft.
The thruster is obviously right at the front while the main engine and domestic batteries are in the stern quarters, I have a 3 stage ac charger for the domestic batteries at the stern, and there is a dedicated ac charger for the bow thruster battery which is right at the front, it was cheaper for the thruster to have its own battery than 50mm2 or so cables run from the stern, the engines batteries are charged from its alty.
In your situation, and maybe others here will agree is to have a seperate power source altogether for your engine instrumentation, a small 12v lead acid battery maybe 2ah, or even aa's, and recharge these from the engines battery, as I assume you only look at the instrumentation while the engine is running, you can get 12/24v chargers off ebay for little cash.
Then your instrumentation would only be associated with the engine electrics not the vessels, which should sort things out.
Sounds like you have connected deep cycle and engine batteries together, not a good idea, really your engine batts want to be seperate, I spose that would mean expense on more deep cycles to power the thruster.
If you dont have domestic loads that much then all engine batts might be better next time you need new ones.
Long leads and heavy loads are an invite to noise, the inductance of the leads causes ringing, but theres no way round that either if the thruster is a ways off, you can get fat ferrite torroids, but I've never seen one you can run a 100mm2 cable through a few times.