Not sure if I can explain this correctly…but here goes.
I am setting up a battery energy gauge for my 3 battery set up. Can I hook all 3 negatives together control the positives thru a 3 position switch and a momentary switch to feed the gauge? My biggest concern is the alternator on the engine and if this set up would affect it being all grounds are connected together. For my 24 volt to the trolling motor is jumped at the 2 batteries. 
That sounds like it would work fine with the three way switch and the isolation.
All of your grounds would go to a common ground somewhere on the boat anyway. I have two main runs on my ProV that are used for common grounds and I never have an issue of anything popping fuses or too much interference.
if you are runing 1 battery for the engine and two for the trolling motors i wouldnt group the neg. together….. you might end up with electrical “noise” on you graphs and radio etc…… group the trooling negs together and the starting barrery sperately.. if that makes sense..
still not 100% sure with out looking at it or a layout of your elec. system, and thats just been my personal experience with the “noise” issue
I don’t see any way to hook all three grounds together….specifically the 24 volt setup for your trolling motor. To get 24 volts, there are two 12 volt batteries in series. In the “middle”, the negative of one battery is tied to the positive of the other battery. In other words, the negative of that battery is 12 volts above ground. If you tie all three together my guess is that you’ll see some sparks and melted wires.
Rootski
If your batteries are wired in series, I think if you
connect negitives you’ll have a dead short.
what kind of trolling motor? 12 volt or 24? thats a good point guys….. or what are you trying to hook up?
I would listen to Rootski! You have a 12 volt potential at the negative battery post on your 2nd battery in a 24 volt system. If you are going to use a 3 way switch make sure you a have double set of contacts on each position. That way you break the positive and negative together,that will keep your positive common wires separate.
Should have added, keep your negatives (commons) separate using the switch.
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I would listen to Rootski! You have a 12 volt potential at the negative battery post on your 2nd battery in a 24 volt system. If you are going to use a 3 way switch make sure you a have double set of contacts on each position. That way you break the positive and negative together,that will keep your positive common wires separate.
This is the route I will likely take.
My question is why would I end up with a short when running two batteries in series? When running on board battery chargers there is no need to separate the two batteries? What am I missing?
Because there is a resistance across the batteries positive and negative terminals with any load (motor, light, radio etc. etc.). By jumping the commons there is not enough resistance across a piece of wire, or like Rootski pointed out there is a dead short.
By the way good one Rootski! 
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When running on board battery chargers there is no need to separate the two batteries? What am I missing?
The reason you can hook up a to channel on-board charger to both batteries in a 24 volt system is because the two channels are isolated from each other. The two negative connections are NOT tied together. They act completely independent of each other, so they don’t care about the connection between the two batteries. If you tie all of the negative sides of batteries together, they aren’t isolated from each other any more.
I don’t think I explained this very well 
Rootski
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