There is nothing particularly difficult about installing two layers of fiberglass cloth at once. It is simply a matter of taking your time and attention to detail. The first thing to do is to get an assistant. That person's only job is to mix a steady stream of small batches of resin while you do the application. That way you aren't rushing to mix batches while trying to apply the stuff and can concentrate on the job. You're also a lot less likely to accidentally mis-mix a batch due to rushing to get back to applying resin. Cloth takes time to absorb resin and the fresher that resin batch is, the better it will absorb, so you want to work with small-ish batches, starting in the middle and working out in both directions or from one end, working toward the other end. Some people do the spreading with a squeegee, I prefer a foam roller, but both will work and you want to use moderate pressure with either one. Too much pressure tends to cause the resin to foam and can trap a lot of tiny air bubbles down in the cloth. Structurally, they're no big deal, but on a clear finish they can show. On a surface that will not get filler coats (like the inside of a stripper) I'll generally go over it after rolling with a foam squeegee. These are just slabs of ethafoam cut about 1/2" thick on the band saw or with a fillet knife. They will allow you to "comb-out" the final cloth texture to a very uniform pattern that's tightly down on the surface, free of excess resin and pretty decent looking despite showing cloth texture.
Bubbles and/or wrinkles are usually caused by the cloth moving a bit as you saturate it. With either a roller or a squeegee you have the ability to create tension, pulling the cloth away from the wood and making a bubble, or by pushing the wet cloth and piling it up, forming a wrinkle. Again, working with small, fresh batches of resin will give you maximum time to address these problems and fix them by moving cloth toward the bubble or away from the wrinkle to spread it back out and get it down tight to the wood where it is supposed to be. Before you leave one small area to work on the next, be sure it is the way you want to leave it, as going back later when the area has started to cure is usually just going to make things worse. It is also a good idea after laying the cloth dry on the hull before you start saturating it to go along with a pair of scissors and trim off the factory woven selvedge edges from the cloth. This will free up the weave a bit, which allows the yarns to move on themselves more and the cloth to conform to rounded shapes better and with fewer stubborn spots, bubbles and wrinkles. If you are doing an additional half-layer over the bottom, you lay that layer on first, then the full layer over it and saturate both at once. That way the resin will go a long way toward filling and fairing the "stair-step" where the hull transitions from one layer to two (fewer filler coats and less sanding will be needed to smooth the transition). It also uses less resin, gives a higher glass and strength-to-resin ratio and adds less excess resin weight to the hull. You don't need to be some sort of fiberglassing wizard to do this. It's just not that difficult if you work carefully, and it can be done on glass as heavy as ten ounces or more on big boats with a bit of care. Double-glass up the sides of a canoe really isn't needed and usually just adds cost and weight. That glass just needs to keep water out unless you're in the habit of hitting things which are well above the waterline. Since outside sheathing adds so little impact strength to the structure, heavy glass up there isn't really going to strengthen the hull much anyway.
Your notion that fiberglass skinned canoes are "stronger" than canvas skinned canoes simply is not true. Fiberglass yarns do have higher tensile strength than canvas yarns. This means that when you grab one and pull on both ends, it will have a higher breaking strength than the canvas yarn. It will also have less elongation (stretch) before it breaks. However, the typical rock impact does not take advantage of the tensile strength of a fiberglass outer skin. Two layers of six ounce cloth makes a skin that is just about as thin and flexible as a plastic milk jug. If you don't believe that, lay up a couple layers on a sheet of waxed paper, let it cure, peel it off and flex it. When a canoe impacts a rock, the hull flexes inward. The outer glass skin bends a little bit, which is no problem (as shown by flexing your test sample or milk jug). It's hardly being stressed at all. The real stress from the impact is on the inside of the hull. The thicker the core or structure and the farther you get from the rock, the more tension and stress there is on the inside of the hull. It will stretch or flex from this tension to a point, and then it will break - long before the outer skin has even been damaged.
In the case of a rib and plank hull, the wooden structure will break long before the glass has even been damaged, and the glass layers are not able to add any significant strength to the wood because they're not being put in tension, which is where their true strength lies. They're just flexing a bit. The strength (and the limits of impact strength) of the wooden canoe is the wood inside, not the outer skin. Whether it's fiberglass, canvas, Dacron, Kevlar or polyurethane saturated monkey fur, it simply is not in a position where it can make a significant tensile strength contribution to the structure on impact. In order to fiberglass the outside of a wooden canoe hull and get a significant increase in impact strength you would need to add almost as much fiberglass as it takes to build a stand-alone fiberglass canoe - and who wants a 15' canoe that weighs 120 lbs.????
If you look through the old Old Town catalogs you will notice that the Trapper was never advertised as being stronger than the Lightweight (same basic hull but canvas covered) or Featherweight (same hull, Dacron covered) models. It was advertised as being "somewhat tougher" on shallow, rocky streams because the fiberglass is somewhat more abrasion resistant than filled canvas, but it was never claimed to be a stronger structure because it is not. Despite the higher tensile strength of fiberglass, in this type of construction if you have the same wood on the inside where the real brunt of an impact will be absorbed (or not - resulting in a break) you will have similar strength. In the case of the OT Trapper, the strength will be that which you can generate with 1/8" thick cedar planking and 1/4" thick cedar ribs.
Much of this will also apply to wood strip/fiberglass boats. It's the same deal only in this case, the outer glass will flex a bit, as before, and the real tension from the impact is borne by the fiberglass inner layers. The thicker the strip core, the more tension those inner layers will get. The good news is that since tension is what fiberglass does best, these layers are in a perfect position to help strengthen the boat. The bad news is that even so, rocks have more strength, so a stripper is by no means unbreakable. One of the most common rookie-strip-builder mistakes is to skimp on the weight of the inner glass. They think "Gee, the rocks hit the outside, so I'll save a few pounds by reducing the weight of the inner glass layers."
"Hey buddy, you may have saved five pounds, but in the process you just gave away half of the impact strength of your canoe, because those inner layers were its main contributor."
The big canoe has two layers, 22' long of 10 oz. fiberglass over the bottom, inside and out, applied at once as stated above. No bubbles, no wrinkles. The drift boat has two layers of 7.5 oz. glass over the bottom, inside and out, applied at once. The Old Town has two layers of six-ounce over the bottom, applied at once.