Eric is probably thinking of Forstner bits, but you don’t need them to drill holes in boat hulls or synthetic gunwales. Regular jobber bits will do fine.
The way I install thwarts and yokes is to first determine the length of the thwart required and trim the thwart or yoke to that length. Sometimes the shape of the hull at the sheerline will dictate that the wood be cut at an angle rather than perfectly square. A hull with sides that pinch in versus one that flares out at the gunwale will require the wood to be cut at opposite angles. A thwart placed between the center and stem requires that the end be trimmed off at an angle that matches the angle the gunwale is making (relative to the center line of the hull) at the point you wish to install it.
When you drill holes through the yoke or thwart, you want to be sure they are far enough from the cut end so they will not break though the end grain. So I often drill the holes through the gunwales at a slight inward angle rather than straight down. I also like to leave a very small gap between the cut end of the thwart and the side of the hull on each side so that the thwart or yoke is not pressing directly against the side of the boat. So take that into account when you trim your thwarts. It goes without saying that for a yoke, or a shaped thwart, you need to trim an equal length of wood off of both ends so that it is properly centered.
Once I have the thwart trimmed and the position for the screw holes marked on the gunwales, I use C clamps to fix the thwart to the underside of the gunwales in the correct position. I place a thin shim of wood or plastic between the cut end of the thwart and the hull on each side to maintain that small gap before I tighten up the C clamps. I then drill starter holes down through the gunwales and the wood all in one go, starting with a bit much smaller than the final size required. The best hardware for mounting thwarts and gunwales are stainless steel machine screws of #10 size. You can get them with 24 or 32 threads per inch (24 tpi is more common) and either will work so long as you have the right size nuts. You can get either flat head or pan head machine screws. On synthetic gunwales I like to use stainless steel finish washers on the tops of the gunwales so that the holes need to be no bigger than the shanks of the screws. You need screws long enough to go through the entire gunwale and the thickness of the wood and still have enough length for a washer and nut. I like the nuts with the nylon inserts. If you are going to install one yoke and one thwart you will need four #10-24 or #10-32 Phillips head machine screws of appropriate length, four #10 finish washers, four #10-24 (or #10-32) nuts with nylon inserts, and four #10 flat washers, all stainless steel.
After you drill your first small holes, loosen the clamps and look at the hole through the thwart. If the hole is not quite centered or is not as far from the cut edge as you would like, you can adjust it a little as you go to larger bits. The final size of the holes in the gunwales need only be just large enough for the machine screws, but I like to use the next size larger drill bit for the holes in the thwarts. The reason is as the wood soaks up oil, varnish, or polyurethane it will swell a bit and the holes will narrow down a little. You would like to be able to remove the hardware and the thwart later without the wood chipping.
Once you have the holes drilled, before you install the thwart or yoke, apply some type of finish to the cut ends of the thwart and to the holes in the thwart to protect the end grain against moisture penetration which will rot the wood. If the thwart has an oil finish you can use oil. Otherwise, I would use varnish or polyurethane. If you don’t already have something, Helmsman’s Spar Urethane (made by Minwax) will work well and can be purchased in small cans. I use pipe cleaners to get the finish down into the screw holes.
Personally, I would not sweat the exact location of the stern thwart. If you want to keep a stock appearance, you can get a good visual estimate of where Old Town positioned it from the many photos of Tripper canoes you can find on the net. Install your center yoke first so as to maintain a center beam at the gunwales of 37". Once you have that installed, measure the inside beam of the hull at the position you want to place your stern thwart to determine the length you want to trim it to.