-- Last Updated: Dec-28-13 10:33 PM EST --
Personally, I don't do anything at all to a canoe to modify it for fishing. If the water you fish is suitable for using a canoe, you may not need to do anything to the boat at all. If you want to come up with clever ways of storing multiple fishing rods, or to rig rod holders for trolling, or something similar, maybe a more specific question would be in order.
One thing to consider is how to anchor, if you need to do that. The kinds of places I take a canoe, I don't need to get fancy with anchoring because I only use a canoe on small waters and anchor only temporarily (on bigger waters I use a very small motorboat, so dealing with two anchor lines is much easier). I usually tie just one anchor line to a thwart and that's good enough, but for bigger water or situations where the boat must not wander in the wind or current, you'll need two. If I needed two anchor lines, I'd just crawl forward and reach back to thwarts far enough apart to "stretch" the boat between them. If you are a big person and can't scramble around in a canoe very well, you could tie a short length of line to forward and rearward thwarts, and put a carabiner or some such thing at the end of each, onto which you'll tie an anchor line. When those short lines are not in use, keep carabiner ends within reach. Tie an anchor line to the carabiner with two half hitches on a bite (a mid-rope loop), pull the boat away to make it tight, and keep the excess anchor line within reach. Later, you can pull that excess line to bring the carabiner and attachment knot back to your seating position to untie it. Do the same for the other line, but whichever is more difficult to work with, tie that one first (and untie that one last).
If you CAN scramble or reach far enough forward and backward to attach two lines to forward and rearward thwarts, you can just run the anchor line under the appropriate thwart and then tie it off close to where you sit (again, with the knot on a mid-rope loop, so there's no need for cleats).
Speaking of anchor lines, this is the one thing that most people could organize a lot better, but don't. The method I learned as a kid is to cut a "rope-storage spool" out of a piece of thin plywood (1/4-inch is thick enough. The thicker it is, the heavier it will be and you don't need that). Make it roughly 16 to 18 inches long and about 5 inches wide. Cut a deep, U-shaped notch in each end. This is a spool onto which you can wind and store your anchor line. You can wind/unwind it easily by hand, and though it's a two-handed process, it's well worth it. You'll never have loose or tangled rope laying around in the boat. Lastly, use good synthetic rope for your anchor lines, a type that's nice and limber, not the cheap, stiff, plastic-like stuff.