Adding an onboard charger

[Broke Pilot]

Why do you say that? I have a very light hum when the engine is running, it gets a touch louder if the blower is on. And the wake plate causes a click in the speakers. I think the head unit is he only thing that needs to have the ground moved. If I remember correctly it's grounded to the bus bar under the dash. When I bought the boat it had 3 noise isolators behind the head unit. When one of them failed, I removed them and now I have the noise.

[MLA]

Those GLIs typically mask a noise, not fix. If the head unit is grounded on the helm BUS, its likely drawing its B+ under there also.

[David Analog]

GLIs are nasty band-aids. They have a few legit applications, like for instance, when mixing AC and DC audio components or isolating grounds between phone chargers and audio inputs. But in most cases they are masking an installation problem that should be corrected.
GLIs use tiny transformers to break the flow of DC between audio components. Inexpensive GLIs induce their own phasing and filtering problems that can hurt the sound quality. People rarely spend the extra bucks to get a really good quality GLI. Fix the core issue and give the GLIs the boot.

[Broke Pilot]

I guess I wasn't incredibly clear on 'rewire all the stereo grounds to the battery'... All the amp grounds are wired to the batts, obviously. The only part that's not is the headunit. It's wired to the ground bus under the helm. And the GLi's have been gone for a while, I know they're band aids, but they were working til one failed and I pulled them.
I put my new batteries in though yesterday and ran across something interesting, the positive and ground for the accessories on the helm are wired to the accessory battery. The cables even have labels zip tied to them that say -accessory and +accessory. So in essence the headunit is grounded to the accessory battery.
So... Now I'm wondering if that's where my noise is coming from now that the GLi's are gone. All the accessories, bilge, blower etc are on the accessory battery, which doesn't seem right to me. Those should be on the crank batt right? But like I said, this is a factory install from supra. They wired it that way. But hat doesn't explain where my alternator noise is coming from when he motor is running.

[David Analog]

It is still going to be very important to run new and dedicated B+ and ground wires of a good gauge from the supply source to the HU or any other source electronics. Here's why. Even though they may currently be routed to the same ultimate destination, you don't know what is going on between point A and B. How many times does that wire change buried in the harness? How many connectors and what type? What gauge wire? What other supplies are carried on that same long run? Exactly how long is that run? That factory harness run can offer substantial resistance. And resistance translates into a voltage change. That's all you need to induce a ground or supply loop.
Now, afterwards you may discover that you have another issue to contend with. But there is little to no chance you will diagnose a second issue as long as the problem is mask by the first issue.

[Broke Pilot]

Very true, thank you... So here is the plan, I'm going to move the accessory battery cables to rhe cranking battery, so that all of the accessories are running off of that one (the way I'm pretty sure it should be). I'll run a dedicated pos and neg to the accessory battery from the HU.
Here's where it gets tricky... Once all the accessory switches are on the crank battery my switch 12v for the headunit will be too. Should I also runs power and ground from that switch to the stereo battery and separate it also? Or is the switch 12v enough to cause noise?

[David Analog]

Many boats do not require this extra step. Many others do corresponding with a substantial audio system upgrade. Many buy cheaply designed amplifiers that do not have the ability to reject this type of noise at the input...or require that they go to excessive lengths to re-route RCA cables (two different issues that better quality amplifiers can impact). My opinion is that when you are executing the upgrade, go ahead and run the extra wiring at that time while it is a painless exercise. Then you are covered in any case.
The next issue often becomes maintaining the original key or switch functionality, while obtaining isolation from the factory harness. One easy solution is to add a basic relay that is triggered by the factory key or switch but interrupts/passes-through the supply from the direct source. These two parts of the relay are totally isolated.

[zd215]

Be careful moving your accessory leads over to the cranking battery. Now items such as your blower, pumps, and lights will be putting drain on your cranking battery. A recipe for getting stranded if you float for a while.

I rewired my VSR setup and entire audio system over the winter and left the accessory leads hooked up to the 'stereo' battery since it wont leave me stranded if i drain it completely. My head unit switch on the helm operates off the accessory lead, that switch operates a relay on my amp board that the head unit is connected to. The actual power feed to the head unit comes from the same distribution block my amps are wired to, which is directly to the 'stereo' battery.

[Broke Pilot]

I like it... Thanks guys. I think I have my plan.

[David Analog]

Be careful moving your accessory leads over to the cranking battery. Now items such as your blower, pumps, and lights will be putting drain on your cranking battery. A recipe for getting stranded if you float for a while.

I rewired my VSR setup and entire audio system over the winter and left the accessory leads hooked up to the 'stereo' battery since it wont leave me stranded if i drain it completely. My head unit switch on the helm operates off the accessory lead, that switch operates a relay on my amp board that the head unit is connected to. The actual power feed to the head unit comes from the same distribution block my amps are wired to, which is directly to the 'stereo' battery.

^^^ Great advice. Not everyone thinks things out to their conclusion like this. And with every different scheme, like a conventional dual battery switch, or VSR, or VSR with dual circuit switch, the wiring may change.