Unless the boat is awfully soft and flexible or it's badly supported (like sitting upright in the back of a pickup truck with a good portion hanging off in space, or with it's weight being concentrated on a couple of small bunks against the hull buttom) I can't see the trailer causing the problem. In any case, having it sit on the gunwale structure has the best chance to spread strain out over a large area when trailering and generous padding certainly never hurts.
There really isn't a single, perfect layup in terms of glass weight. Bigger boats benefit from heavier glass than small boats need and wide boats may well need more glass weight than narrow ones to generate adequate bottom stiffness. If we're talking about regular, common weaves of fiberglass cloth and boats in the 15'-18' range, I've always had good luck with a full layer of 6 oz. inside and out with a second layer over the bottom, both inside and out (both layers applied at once with the "bilge-cookie" partial layer next to the wood core). It doesn't make an ultralight boat, but is usually lighter than most other canoe materials and has enough durability to survive hitting that occasional hidden rock with little more than a scratch to show for it. On really big canoes, I've used up to ten ounce cloth (doubled on the bottom) with half-ribs glassed into the bottom to keep bounce down. Solo boats, racing canoes and little boats like Wee Lassies can also use the "standard" six-ounce, double-bottomed layup, but you can save some weight by going to lighter fabric. This does come at a durability price though, so the builder needs to be a little more careful with those lighter boats.
You also want to minimize bounce. There is nothing wrong with a little flex if you hit something (though stripper construction in general doesn't make particularly flexible hulls) but hull flex and bottom bounce in open water is bad. Every time a hull flexes or bounces, fibers are stressed, stretched and/or broken - both glass fibers and wood fibers. They don't grow back. Each time the hull bounces or flexes, a few more die and the hull gets a little bit softer (and more prone to more bouncing). The old fiberglass whitewater kayaks were a great example of flex damage. When you would slide over a rock or ledge, the area right under the seat (where your weight was concentrated) really got flexed inward big-time. After a couple seasons of shallow water boating you would have to go in and add extra layers of glass on the inside of the hull under the seat, because the area had become so soft from repeated flex and the resultant fiber damage.
No matter what weight/durability range you're shooting for with your stripper, you need enough hull stiffnes to limit bottom bounce and the damage that it will eventually almost certainly cause. Unfortunately, I don't think anybody has published any formulas for strip size and glass weight vs. boat beam, bottom shape, etc. Thicker cores are stiffer than thin cores, heavier glass weights are stiffer than lighter weights and more importantly, stronger. If the bottom does get flexed, they're more able to take it without breaking, as well as more able to limit or prevent flex in the first place. Wider, flatter bottoms are less rigid than rounder, narrower ones and may need more reinforcement, just to hold their shape. As you can see, there are a lot of variables and practice and past experience seem to be about the only way for a homebuilder to really get a feel for just how much fiberglass weight a given design will need.
Personally, I never ever use layups that are lighter on the inside of the hull. I generally match the inside and outside layers of the sandwich or in some cases, as mentioned, beef-up the inside even more. Think of your stripper hull as if it was an I-beam. Two fairly light load-bearing plates (the inner and outer glass skins) held apart by a non-compressable core (the strips). If we apply a lot of force to the underside of an I-beam, it will eventually start to break. What will likely happen is the bottom plate will bend (in compression) and the core and top plate will rupture (the core will crush and the top plate is in tension and will stretch until it breaks). Our bottom plate is just being bent, and not even that much, but the core and inner plate are being destroyed. If we then decide to save weight and we make the top plate only 2/3 as thick as the bottom plate the beam is going to break even easier. The same thing is basically true on a strip canoe with a lighter interior lay-up. Switching from 6 oz. cloth to 4 oz. cloth on the inside (top plate) reduces the ability of the boat to survive force applied from below (water pressure and/or rocks). The six oz. outside is going to get flexed or creased some, but like our I-beam's bottom plate, it gets off pretty easily. The other layers get the real stress. Other than a slight gain in fabric and filler coat thickness to possibly protect a bit better from rock abrasion, the outer layer isn't in a position to add much strength in terms of something trying to push in on the bottom. Essentially, the boat isn't much stronger than it would be with four-ounce cloth both inside and outside. It would actually be stronger inside-out with the 6 oz. forming the top plate of the I-beam. The ideal layup is probably something with more glass weight on the inside and the inside/outside cloth weight ratio would need to be coordinated with the thickness of that particular core and how far apart it spaces our top and bottom plates. Until somebody does a whol lot of work and gives us those formulas, it's generally pretty safe to match the inside and outside skins on most canoes and less safe (sometimes a lot less safe) to skimp on the inner layers.
