ctort-
The hull of the C-Dorys is cored, meaning that it has a layer of little 1" square balsa wood blocks between the outer and inner glass layers to build up structural strength by increasing the thickness of the laminate.
As such, sound waves cannot be transmitted through the hull, unless one is willing to drill out a section of the inner layer, dig out the balsa, and replace it with solid resin to render the resulting solid hull transparent to the sound waves from the transducer. This is a little scary for most!
Most folks therefore mount the transducer(s) to the outer end of the transom. In order to reduce the number of holes, a "transducer mounting board" is often used.
This is a piece of plastic (either Starboard or HDPE (high density polyethelene) (cutting board material) that is screwed to the transom in order to minimize the total number of screws placed into the hull. Once it is mounted, transducers can be replaced, a second one added, other hardware mounted, etc. Look up "transducer mounting board" in our Search engine.
The other possible alternative would be to mount the transducer on one of the trim tab plates. I know Red Fox has done this, mounting it within a hole cut into the plate to make it flush, but I'm not aware of any problems or cautions that might be involved.
One has to be careful not to get extraneous echos from surrounding underwater structures when mounting transducers. Also, it is important to get good, solid water flow at speed w/o a lot of air bubbles or extra turbulence which can cause problems with transducer performance.
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The placement of rod holders depends a lot on what kind of fishing you'll be doing, and whether you'll be using downriggers, etc.
Rod storage can be done by adding "rocket launchers" to a radar arch, by adding a stand up rack on the starboard side of the rear of the bulkhead (side w/o the open door folded back), or by mounting them on the top of the roof inside the cabin (less common).
Tyboo has designed a great rack and cover for the bulkhead mount that you can see here (link comming after access to photo albums is fixed).
I'm sure others will add to this discussion soon. Congratulations on the new boat, welcome aboard the C-Brat ship, and good luck!
Joe.