Just push it down into a blob of the sealant and leave it. Before seating the transducer, make sure the top of the sealant is rounded into a dome so you don't trap any air bubbles.

I did this a few years ago when I got the new Lowrance MFD. It came with the fish-finder module and transom-mount transducer, which I stuck down to the bottom inside the boat. Works great, even in 100-foot+ depths.