There are many ways that work and there is no one best in all cases way.  The suction cup is fast and easy but comes off at times Outside the boat will cause drag so you will want to remove it on travel days.  Because they cause drag people tend to put them as near the surface as they can and this can cause some problems.  Picture this you are putting the transducer on the right side of the boat.  You lean slightly to the right as you mount the transducer right at the surface.  Now you move back to the center of the boat and turn on your detector to find it does not work well at all.  If someone were paddling alongside you they could see the puck in just out of the water but when you lean over to check the boat tips and the transducer is back in the water.  If you use a over the edge mount make sure the puck is in the water.
I far prefer a semi-permanent through the hull mount. Chose a spot on the floor of the canoe where there is no foam core or extra material.  Most Wenona and Bell canoes have much of the floor covered with a foam covering much of the floor but usually there is a single layer floor in both ends. There are several products that will work to carry the sound through to the water and back to the transducer.  I have used epoxy, silicone weather calk, bathtub caulk, and my favorite is electrical putty.  I think electrical putty and plumber’s putty are the same with different labels on the package. You want as little space between the puck and the floor of the canoe as you can get and you want all that space filled with putty.  The way I put my current transducer in was to take the canoe out in the grass and set it in the shallow grassy ditch in front of my house.  Place a square of putty about 2” X 2” X ½” on the transducer bottom.  Set the transducer on the floor where I wanted it and stand on the transducer for at least 30 seconds.  Then with my finger work the putty that squirted out up against the transducer making the puty taper from the top of the transducer out to the floor of the canoe.  Anchor the cable so it won’t get caught on packs and jerk the transducer free. My transducer stayed mounted this way without remounting it for several trips from Chicago to Quetico.  I have mover it from on canoe to another and back with by just reforming the putty and sticking it in another canoe.
Magnets are HEAVY!