I have been looking at a dragonfly as well and have a older model Hobie pro angler. i'm thinking about doing the duct seal through the hull install as well, what is the point of putting a little water in there with it?
The idea is to make a well (ring) of duct seal. The bottom of the well is the plastic bottom of of the kayak. When you fill this well with water the transducer shoots through the water, through the hull with no chance of an air bubble between the transducer and the hull. Air is compressible (water is not) and so it kills the signal.
The other way folks sometimes use duct seal is to make a blob and push the transducer into the blob. However, when doing this you risk having some small pockets of air trapped in there that will hurt the signal strength.
Fish tremble when they hear my name
A ship in harbor is safe -- but that is not what ships are built for.
--John A. Shedd, Salt from My Attic, 1928