-- Last Updated: Nov-14-12 1:25 PM EST --
There are lots of ways to outfit canoes for whitewater and everyone has their own preferences.
I think having at least a couple of anchor points (one for each paddler) on the hull bottom to secure gear is an excellent idea for any boat used in significant current. You will at least have a couple of water bottles and perhaps a dry bag or two and you would prefer to not have them loose in the boat in case of an upset.
Some folks will tie or secure gear to seat frames or thwarts which isn't a great idea for a couple of reasons. One, the cords present an entanglement hazard. Second, if you ever have to invert the boat to carry out a boat over boat rescue this junk hangs beneath the gunwales of the inverted canoe and gets in the way.
I have had good results with vinyl adhesive (aka "Vynabond") if used properly but it may work loose after a few years. If so, vinyl patches can usually be resecured with vinyl adhesive. Some whitewater boaters who absolutely don't want their D rings blowing out during some remote run will use epoxy (West System G Flex preferred for Royalex), but it is more expensive and makes it difficult to remove the patch without damaging the canoe if you ever want to.
I would first carefully mark the position of your patches and trace an outline with pencil or a marker. Lightly sand the hull surface with 100-150 grit sandpaper and clean it with acetone or MEK if you have any, or alcohol if you don't. Clean the patch bottom as well and apply an even coat of vinyl adhesive to both patch and hull. You need to let the adhesive "degas" before approximating the patch to the hull which usually takes 15 min or so. You can speed it up by carefully warming the patch and hull with a heat gun or hair drier. Be careful to align the patch as you won't be able to move it after it makes contact. For best results go over the patch with a small, hand-held roller.
I prefer running flotation bag lacing through holes drilled just below the gunwales as it is clean and least expensive and doesn't weaken the gunwales. As Eric said, it does take some time to remove and re-lace the cordage if you want to do so frequently.
If you don't want to do this you can buy lacing kits with nylon "inchworms" to secure to the gunwales with either pop rivets or stainless steel sheet metal screws. Cheaper is to buy some nylon "P clips" of the type used to secure coaxial cable to a wall. Radio Shack has them. You can rivet or screw these to the underside of your inwales or to the hull side just below the inwales. I like 3 mm nylon accessory cord for lacing in flotation bags.
You need some type of "keeper strap" or cord to keep the bag pushed up in the stem of the canoe otherwise water will float it back toward the center. Just about anything will work but I like either 3/4" or 1" wide flat webbing of either nylon or polypropylene secured using nylon "Fastex" triglides, ladder locks, or side release buckles made by Nexus and others.
There are a couple of other modifications you might consider making for whitewater use. I would glue in two pairs of kneeling pads so that you can get down on your knees quickly and easily when you want or need to. Some people prefer to use loose, removable kneeling pads or mats. I find that the large kneeling mats are heavy, and loose knee pads are one more thing to carry to and from the river, to forget, or to float away in case of an upset. Loose pads also are usually not where you want them to be if you need to get down on your knees quickly.
You can buy fancy, contoured pads or just make your own out of 3/4-1" thick minicell foam. Harbor Freight also sells some thin sheets of inexpensive foam which can be glued together in a couple of layers to make pads. Use a good quality flammable contact cement like DAP Weldwood to glue them in. Since foam is somewhat porous you need to use 2 or 3 coats on the foam.
You might also want to add grab loops to the bow and stern stems of your boat since Wenonahs usually lack them. They are handy for securing painters or securing your boat for cartopping. You can tie a painter on to a carry thwart near the stem but it is better to have it lower and closer to the water. You can use a length of 5/16-3/8" thick braided nylon rope or 1" wide tubular nylon webbing for grab loops. Just drill a pair of holes through the hull on either side about 1 1/2" back from the stem and high enough so that your loop doesn't drag in the water. Run a length of rope or webbing through the holes with a knot on either end inside the boat.
You can also run a short length of 3 mm accessory cord through each pair of holes and tie it to itself inside the hull so that it forms a loop under the deck plate of the canoe. These loops are convenient anchor points for you flotation bag keeper straps. Just run the end of the strap around the loop and secure it to itself with a nylon triglide.