So, originally I mounted my transducer inside the hull with goop. It worked pretty good as I had nothing to reference it by except videos on youtube. At one point, when I was out fishing a couple of weeks ago, I noticed that when enough water was in the hull to cover the transducer it worked a lot better. So I've seen where others have made water boxes for their transducer so I decided to make one around my transducer.
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I took it out yesterday to test it and it gave me a much more detailed image of what was under the boat.
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So I recommend this if you don't want to mount your transducer outside of the kayak.