Hi JP: Probably a little late in this answer, but if you haven't mounted the shoot thru the hull 200/83 kHz transducer, here is what I do.
I use a heavy duty baggie 1/2 filled with water and lay it in the chosen spot in the hull. Put the transducer on top of the baggie and then but another baggie 3/4 full of sand on top of the transducer to hold it in place. As long as the inside of the hull is relatively smooth, this will acoustically bond the transducer to the hull with very little air trapped between in. Take the boat out into 20' of water or more (deeper is better) and then see what kind of bottom echo you get. Turn down the sensitivity until you can just pick up an echo. Now try moving the baggies and the transducer around until you get the strongest echo. Once you find the "sweet spot" try several high speed runs and see how it works at speed. It will take some trial and error, but this method, lets you see how and where it will work before you "PERMANENTLY" bond it to the hull with epoxy.
Please note that shoot-thru-the-hull transducers will not work well if there is air trapped in the hull (IE: either wood or foam cored fiberglass hulls)
As far as the SI transducer on the transom, yes that can be damaged by high speed runs or jumping waves or wake. I would not mount it below the hull as the shoot-thru-the-hull transducer will look after the high speed readings and the SI transducer only needs to work at trolling speeds.
Hope this helps-good luck
Keepin' your Birds a "hummin" is Job One!