I have typically just attached the transducer to the side of the hull using the standard suction cup bracket. It sticks out a bit so you have to remember that it is there. Any rolling motion can cause substantial changes in readings. On the kayak I just finished I mounted the transducer inside the front compartment on the centerline.

The transducer can have some problems shooting through wood and the fiberglass/wood interfaces may be a concern as well.

To make a "window" for the transducer, I cut a hole through the bottom and cast a plug of resin to replace the missing wood. Then glassed the hull and added a patch of glass inside to the lock the plug in place. The transducer bracket was mounted to the wood bulkhead, you could use small block of wood epoxied in place if your bulkhead is foam.

If there is an air gap under the transducer you will loose the signal so that needs to be addressed. For ice fishing, putting the transducer in a plastic bag with some water and anti-freeze allows taking readings through the ice but I wanted something a bit more permanent.

The "skimmer" style transducer I have has a rounded face. To get a proper fit/interface, I made a dam (out of a plastic margarine container) around the "window" in the bottom, wraped the transducer in Saran Wrap and copied the shape with some more resin - taking care not to glue the transducer permanently to the hull.

A bit of water under the transducer gives a good signal. Mount the depth sounder and go fishing.

Hope this helps.

Hank