If you are going to shot through the hull you need a place that is solid glass with no voids or air between layers. You could not shot through your water ballast area. Once you find the area build a dam (Cardboard taped to the glass works) around the place you want the transducer to mount and fill the area with something that will not allow air. I read you can put the transducer in a bag of water, but I did not get good readings this way. Vaseline worked for me, I have also read about marine grease, but never had it handy. After you have a good test with the location it is time to permanently mount it. Take down the dam and sand the area to clean. Put up another dam and mix glass resin, hold the transducer in the resin until it sets, it is faster than you think so get it held to the bottom and hold it there using the wire to hold it down. Once it feels solid let it cure overnight and test again.
Good luck.