I just went through the same thing for my new Raymarine Dragonfly 5Pro ff which also has a long chirp transducer. I ended up mounting it on a Ram Transducer Arm, off a rail-mounted Scotty base, using their Hobie/Scotty wedge adapter. Several base and transducer options are available, see
http://www.rammount.com/products/kayak/transducer for possibilities.
Pros:
Fairly quick install.
Ram B-ball joint at the top railside makes it easily adjustable.
Arm is immediately adjacent to seat, making it convenient to keep fish from tangling (or pull the arm up if necessary).
Cons:
Difficult to transport due to having to rotate arm inboard, or disconnect the ball.
Arm is clumsy in the folded state.
No specific mount available for the Raymarine transducer, so I had to use their generic mount which only has 1 point of attachment. Yours may be able to use their LSS adapter?
Compared to my old Eagle ff, this chirp unit is unbelievable though. Yesterday was my first day out on the lake with it. Just messing around getting used to the settings when I spotted a large arch 170 ft down in 174 FOW (good resolution from the bottom using factory settings!) Popped a quick waypoint on the plotter function and pulled out and rigged my jigging setup as I blew downwind. Set a navigation course back to the waypoint and got right back on top the mark in short order. Watched my jig go all the way down and was amazed that I could clearly distinguish the snap swivel 2 ft above the jig from the jig itself, all the way down to the bottom. A few quick jigging strokes and I had a very nice lake trout on the line which was invited home for dinner. So despite the compromises of a rail-mounted in-water transducer, I am confident that this chirp thing will improve my fishing.
Good luck with your setup. Keep us informed on how you rigged it and how it works out.