I will try and address as best I can with the limited knowledge of your exact configuration. First use good heavy wire for both the battery connections to the switch and the jumper that you will place between the negative terminals of the batteries Starter jumpers from an Auto parts store are best with crimp on connectors. This will be the only common connection the batteries share other than the selector switch. Coat all connection with Dielectric grease or anti seize and you will have no regrets. Second you can take all the connections off the battery you currently use and connect all of them to the common terminal (both) of the selector switch. Third connect the primary (starting battery) to the terminal labeled Batt 1 of the switch. fourth connect the second (trolling) battery to the terminal labeled batt 2 of the switch. fifth connect the negative terminals of the two batteries together and anything that is already connected to the negative terminal of your present battery leave it connected to the negative terminal of your present battery. Most of the electronics on the boat are low current consuming devices and it will not make a difference where they are connected. There will be one large wire connected to the negative terminal of this battery and it is very important it remains connected to the main battery. This is the negative wire for the starter of the big motor and it will be drawing its starting current from this cable. The smaller wires can be connected to either battery negative as needed as they carry much smaller currents and won't be effected either way. Now for the fun use the batt 1 position of the switch for starting your big motor. You can also run electronics in this position without a problem. Use Batt 2 position for the trolling motor battery and you can run your electronic in this position also without a problem. Don't start the big motor in the Batt 2 or both position unless it is an emergency as a trolling motor battery is not internally designed for this type of current draw and will degenerate the plates quickly which will limit their charge capacity quickly. Significantly reducing the life span of the battery. Don't run the trolling motor in Batt 1 position as this is the main cranking battery and the one you depend upon to get you back to the ramp or out of harms way quickly. The both position should be used in emergency cases say when for some reason the main cranking battery dies for no reason and you are ready to go home, and don't want to try and pull start a 100 hp motor. I will sacrifie a little deep cycle battery life to get home without pulling on a big hunk of outboard. In the emergency case switch the switch to Batt 2 crank the big motor and head for the ramp. I have but don't recomend running the switch in the both position as the trolling (deep cycle) battery will be charged to rapidly and this will do as much damage as discharging it to rapidly. I only did this on a long day of fishing when I was running between spots and took a chance of frying the alternator in the big motor just to gain a little fishing time. Dumb idea and I know better. I got a buy that time but may not get so lucky next time and don't advise trying it even once.