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You right in saying that it has to point to the bottom. If you look in the pictures below it shows how the ducer on mine has to point. The bracket that came with the ff is pretty good IMHO.
The way ive mounted my transducer is not the best way I know but ive not had any problems yet.
From what I've read you can mount transducers inside the hull of the Kayak and they work fine, the key is to mount it in a big splodge of silicone type adhesive so there is no air between the transducer and the hull, there must be no bubbles in the silicone.
Some fit a bit of foam tube to hold the transducer in position inside the kayak, which is then filled with vaseline and the transducer fitted inside the tube so its in full contact with the vaseline, again making sure there is no air bubbles.