First, if you plan to kneel with your feet under the seat, you must allow sufficient heel clearance to allow easy egress. When you decide how much heel clearance you need, take into account any and all foot wear you might be using. Some paddling shoes and boots have thick rubber soles with heels that stick out a good bit. If you plan to drop the stern seat 4", I think it is very unlikely you will have sufficient clearance. When you measure for clearance, keep in mind that canoe bottoms are not flat. Don’t just measure the rise above the canoe bottom at its center. Measure where your feet are actually going to be.
Second, the paddler’s center of gravity will nearly always be well forward of the center of the seating area regardless of whether they are sitting or kneeling. I have outfitted many whitewater canoes, which are nearly always paddled kneeling, and when I position the pedestals I figure the paddler’s center of gravity will be around the location of their navel, to one inch in front of it. Take into account how you plan to use the seat as a support when kneeling. If you plan to sit mainly on the seating surface your center of gravity will be further back than if you simply brace your rear end against the front cross member of the seat frame.
A seated paddler typically has their center of gravity well-forward of their navel, since their legs are out in front of them. Take a look at solo canoes with symmetrical hulls. The seats are virtually always placed so that the center of the seating surface is aft of the longitudinal center of the boat. To position seats for either a seated or kneeling posture, I usually figure the paddler center of gravity to be 1 1/2" forward of the front of the seat frame. This rule of thumb has worked out well for me when trimming canoes.
Many, if not most tandem canoes are trimmed significantly bow light at the factory. Part of this comes from a desire to provide leg room for a wide variety of bow paddlers. The stern seat is often placed as far rearward as the gunwales will allow to provide clearance for carrying cargo. I usually prefer a neutral trim, but many prefer a slightly bow-light trim. One method to determine seat positioning for a tandem canoe is to first determine the placement of the bow seat. This will depend on the amount of leg clearance the bow paddler requires or desires. Place the bow seat as far forward as it can go while still allowing for sufficient leg room. Then determine the placement of the stern seat. If you want to do this with more precision than simply guessing the paddlers’ COGs and using a formula based on paddlers’ respective weights you can do the following but it is a little laborious and will require both paddling partners and a third person as an observer.
First float the boat in calm water without seats. Position some 2 inch strips of duct tape at the bow and stern so that the bottom edge of the tape is right at the water surface. Install the bow seat. Find something like a bag or milk crate that you can use as a temporary stern seat that will position the stern paddler at roughly the desired height. Now have both paddlers get in the boat, the bow paddler on the installed seat and the stern on a temporary seat that can be moved forward or aft. With the paddlers assuming a normal paddling posture, have an observer note your trim using the tape strips as a reference while the stern paddler adjusts the trim by sliding the seating surface forward or back. If you want a neutral trim, adjust your position so an equal amount of tape is peeking out above the water at the bow and stern, otherwise you can adjust for a slightly bow-light trim. When you are positioned for your desired trim. place a tape strip on the gunwale at each side of the stern paddler in line with some particular part of the paddler’s anatomy, such as their navel. You should be able to figure out where to place the seat to put that part of the stern paddler’s body at the fore and aft location.
I have done this a number of times but I have found that the rule of thumb I described previously gives the same results with a lot less trouble. Exact seat placement does depend to some extent on paddler anatomy, however, especially femur length.