Man it's great to have the resources that you guys provide. It would have made it easier if Yamaha would have just put the gauge on the cable!!Looking at the diagram of the switch, I am assuming that it is a 1/2/1+2/Off type switch, and then the cluster has the VSR relay in place so that when the engine is running and the alternator providing a charge that it can switch the charging over to the 2nd battery to top both off. With this type of setup, you are cranking your motor AND running all your "house" loads (lights, pumps, electronics, etc) off the same battery - and you manually change the switch to run off the other battery. In that setup, good practice is to change the switch every trip - so that you alternate which battery you pull from. As a rule, you do NOT run the switch in the 1+2 setting unless you need to parallel the batteries for reserve cranking power - i.e. both have gotten drawn down individually too low, but combined they'll get you home.
The switch is a 1 or 2 type switch, I don't believe it has the 1+2 option? The VSR will automatically switch to the lower voltage battery after the switched battery is charged. So I should always have a charged battery no matter what the position. As long as the boat is running it will charge.One thing to note with this setup - you are using a cranking battery, which is meant for high surge amps but not long, constant draw, to power your constant draw items - lights, stereo, bait tank?, etc. This is tough on the battery over time - in that scenario you would ideally use a dual-purpose battery like an AGM - that can do both cranking and deep-cycle.
I have a cranking battery and a Exide 900 mca deep cycle (for the house loads).Or, you set things up with two batteries - one for cranking, and a separate deep-cycle battery for the "house" loads, and have a switch that can parallel the two if needed..... keeps loads off the cranking battery, but you still have some reserve capabilty. I also keep a pair of jumper cables on the boat in the event I need to use one of the trolling motor batteries to help get things headed home in a real pinch.
I do not have a trolling motor yet. I working on that purchase also. Dang kids need clothes & shoes, who thought?But sorry - I digress
No problem, you can never take in to much knowledge.Use
marine-grade, tinned, stranded wire for all your connections. Use
crimped lugs - not solder. The delta in price is not worth the hassles you'll have down the line - especially if the boat gets near salt at any time.
A couple of great sources for wire & terminal ends and very reasonable prices and pretty quick shipping are:
www.genuinedealz.com/gregsmarinewiresupply.com/Zen/When I rewired most of my boat the other year, pretty much all my supplies came from one of the two of these. GenuineDealz & Greg's can actually go ahead and make up the cables for you if you know the length and specify the ends you need - you just need to know exactly the length you need - hence I ordered wire + lugs and cut/crimped myself so that I could fine-tune the lengths given I was cramming a lot into a small space. But having them do it saves you needing to have access to a proper crimper - which for larger cables you'll need a hydraulic one to do it right - you can get by with the anvil type, but they don't do near as good a job as a hydraulic one - but hard to justify a hydraulic one for just a couple of cables - even with the "cheap" one you can get a Harbor Freight.
I'm assuming you will be locating the two batteries next to each other. and that you are still using the wire that went from the motor to the battery to now connect from the motor to the switch? Should be fine to leave it as long as the wire is long enough to reach - it would have been sized for that length of run.
Everything will fit in the same compartment that the engine cable is already present in.For the wire running from the each battery to the switch, use 2 gauge.
Is this #2 awg or 2/0 awg ? It's possible that on the 115 you have 4 gauge to the motor, but nothing wrong with bigger other than it is a little less flexible to work with and just cost a few dollars more for the amount of wire you'll need, plus you will be pulling any loads at the same time you pull the motor cranking through that wire - while it should only be for a short time that the maximum load is seen (while you are cranking), it is just another reason to use the larger wire.
Ground to the motor will just connect to the terminal on the battery, using existing cabling from the motor assuming it is long enough.
Good there.Use a 2 ga wire to connect the two battery ground terminals. Lug connections - not the "car" type battery connections. Use a hex-nut (not a wing-net) with the nylon insert that keeps the nut from vibrating loose to secure all connections at the batteries.
To your breaker panel, it would be best to know the loads that you are powering off your panel - and is anything else powered that is NOT through the panel, and the distance of these runs. Ideally you want to run the numbers to make sure your voltage drops across the run is acceptable - ABYC specs 10% voltage loss for general lighting and non-critical systems - 3% for power to panels and switchboards, navigation lighting, bilge blowers, main DC feeders, and any other circuit where voltage drop should be kept to a minimum (electronics).
There is a voltage drop calculator here:
www.genuinedealz.com/voltage-drop-calculator Also, a table to cover maximum current draw on a given size conductor.....
If you have 10 ga running to your panel, then its spec'ed for a max of 60 amps. If you're just running basic lights, finder, a "normal" stereo, etc, then you should be OK with that - though you'd want to run the voltage drop numbers as that may push you to be in a larger size wire to minimize loss.
You should have a breaker or a fuse on the positive wire feeding your panel, within 7" of the switch. No need for a breaker or fuse on the wire going to the motor - the motor is fused on it's end. And if you are going to have the switch within about 12" of the batteries, then you're OK - 7" is the recommendation but it is almost not practical to accomplish with two batteries and the turn radius of larger gauge wire.
Fuses are present at the batteries for the house & starting loads.Does your panel consolidate the ground returns from all the loads or do the grounds run back to a ground bus-bar somewhere? You need to make sure the ground that comes back to the battery is property sized. If the only loads are supplied off the panel and the panel has a 10 ga wire, and all grounds come back through a consolidated point (bus-bar, other), then I'd use 10ga there as well - or you probably already have this in place.
Looks like there is a ground connection off the VSR that needs to be connected (the yellow highlighted in the pic). I should not matter where you connect it as long as it is, as you must have all your ground terminals connected together.
10ga?A couple of other notes:
- bilge pump - Assuming you have an auto-bilge pump - the positive side of this should be connected DIRECTLY to the battery through its own fuse - NOT to the switch - you want the bilge "hot" all the time. I used the blade type fuses in a marine-grade (tinned, stranded wire) water-resistant fuse holder.
- stereo memory - if you have a stereo that requires an always-on connection to keep memory for time, pre-sets, etc (often a yellow wire), then this needs to be connected to the battery as well (or you can connect it to one of the terminals on your switch to which the battery is connected - it should ideally be fused also, but can be fused with something like a 3A fuse)
I need to add this the stereo has to be reset every time we use it.I will send you the pics when I get it all hooked up thanks again to you guys for the information. Got to get this done I think spring is on the way now??? 
genuinedealz will even make up the cables for you pretty quickly if you don't have a big crimper.