Rod,
A lot of people are switching over to lithium and really like the benefits of lighter weight and more usable capacity. There are pros and cons.
As far as three 12 volt versus one 36 volt battery, here are a couple things to consider. With a 36 volt single battery you lose the option of hooking up other 12 volt accessories to this pack. In my case I run two 156 AH lithium batteries for my 24 volt Ulterra and have my electric anchor hooked to the one and my Garmin navigation to the other. The rest of the 12 volt electronics, live wells and bilge pump are hooked up to my AGM starting battery. With the larger electronics like we have today you could be drawing 2 to 5 amps just to run the electronics depending how large and how many you have. This could deplete the charge in your starting battery especially if you aren't running the outboard enough to replenish some of that charge. A higher capacity starting battery, like 90 AH or more, would be a good idea if you are running lots of electronics and don't want to get stranded on the water. Another option would be to have an additional 12 volt deep cycle battery designated just for electronics.
With the newer multi-bank on-board chargers it is not an issue to run 12 volt accessories off of your trolling motor batteries because the charger will recharge each battery individually to 100% again keeping the bank balanced.
Another possibility with lithium is that you can run out of power without any warning. The internal Battery Management System (BMS) will cut off power when the cells are discharged. If you have a trolling motor like an Ulterra that deploys and stows on its own it will be very unhandy when your lithium pack is discharged because you will have no power to stow the motor. I speak from personal experience Lead acid or AGM batteries will generally fall off slower towards the end of the charge and you will notice slower speeds and still have enough power to stow the motor.

Let me summarize by giving some pros and cons of each battery chemistry...
Wet cell (flooded) lead batteries.
PRO's - Lowest initial cost and cost per AH. Easily recycled. No special charging system required. Recharge at any temperature.
CON's - Heavy. Maintenance required. Corrosion issues. 3 to 4 year life on average. Usable AH is about 60% of rated capacity.

Absorbed Glass Mat (AGM) lead batteries.
PRO's - Sealed maintenance free design. Dual purpose for Starting and cycling. Easily recycled. Recharge at any temperature with AGM compatible charger.
CON's - Heavy. Higher initial cost and cost per AH than wet cell. Cycling life about 3 years, Starting application about 5 years. Usable AH is about 60% of rated capacity.

Lithium Iron Phosphate (LiFeP04)
PRO's - Usually 1/3 the weight of a lead battery for the same AH. 2500 plus cycles give 8 year or longer life expectancy. Recharge in less time with higher amp charger. Usable AH is 90 to 100 percent of rated capacity. Low cost per cycle over life of battery. Maintenance free.
CON's - Much Higher initial cost and cost per AH. Recharge with LiFeP04 compatible charger and only above 32 degrees Fahrenheit. Expensive to recycle.

Hopefully this is helpful for someone that is considering their options to power their boat. I know it is much more than what you asked for Rod, but I own a battery company and just wanted to give back to everyone on this forum in appreciation for all they have contributed to make me a better walleye angler.

Blessings! Lynn