You don’t necessarily have to place the seats in the “stock” position. Where you place them depends on how you plan to be using the canoe, and who you plan to paddle it with.
The more distance you have between seats, the more room you have to carry gear which may or may not be an issue. Other constraints are how close you can physically position the stern seat to the stern stem and how much leg room you want or need for the bow paddler.
In my experience, many tandem canoes are set up stock to be trimmed significantly bow light. This is probably better than taking a chance on them becoming trimmed bow heavy as a result of a big discrepancy in paddler weights, but most are more bow light than I prefer. The MRC 16 foot Explorer is no exception. My Explorer is a Kevlar version, but I think that the Royalex version has seats similarly positioned.
In your case, a position of the stern seat center 36" from the stern stem sounds awfully far aft. The Explorer does have fairly full ends, but I would question whether the width of your rear seat seating surface will allow you to fit it between the sides of the hull that far back. If it does, consider whether this position will allow you a comfortable degree of leeway between the gunwales to fit your body, or the body of the likely stern paddler. Keep in mind that the distance from the front of the front seat frame to the rear of the rear seat frame of the typical wooden frame canoe seat is only some 9 1/2" give or take a smidgen. The typical width of the seating surface is around 12-13", but sadly the rear end of many a modern paddler will extend beyond that by an inch or more on either side.
I usually start by deciding how much leg room is required for the bow paddler. The distance aft that the bow seat needs to be placed is usually determined by this factor. I also figure that for the average paddler in an upright seated position, the body center of gravity typically winds up to be around an inch and a half in front of the front edge of the seat frame. The paddler’s center of gravity will depend on how they sit on the seat, how much they stretch out their legs, and if they lean forward the COG will of course shift forward a bit.
Once you determine your bow seat position, you can decide where to place the stern seat. If you anticipate paddlers of roughly the same weight, and you want the boat trimmed neutrally, measure the distance of the front seat frame from center, add 1 1/2", measure that distance aft from center, and place the front of the rear seat frame 1 1/2" further aft. If you anticipate the stern paddler being significantly heavier than the bow paddler, you may wish to position the stern seat further forward. If you want the boat to be a bit bow light, you can shift it a bit aft.
As an example, given the schematic referenced by RLS assuming a 16 foot explorer, the very front of the front seat frame from center in the stock position is 38.5" and the front edge of the front frame for the rear seat is 50.5". If you use my rule of the paddler center of gravity being roughly 1 1/2" forward of the front edge of the seat frame, the bow paddler COG will be 40" from center and the stern paddler COG will be 49" from center. The stern paddler’s COG being farther from center, the boat will trim bow light for paddlers of equal weight, which is exactly my experience for that particular boat (and many others).
If you want the boat trimmed closer to neutral for paddlers of roughly equal weight, you can either move the front seat further forward (as the requirement for paddler leg room allows) or the rear seat further forward, or a combination of both. Moving the rear seat forward is usually easy to do but will diminish somewhat the space available to stow gear.