2D-only transducers are fine shooting through the hull. But you'll lose some definition if your try to stick HDI or SI/DI transducers inside. Mount it on the transom. Doesn't have to be that low. Just has to be comfortably under the water line. Mine is a good 8" from the bottom of my transom, which limits the risk of it being knocked off. It also limits it's SI range on the side it has to look past the motor, but I don't really care about SI that much.
What do you mean "run the old wires"? Are you talking about power? If so, that should be fine I would think. Anything else, you'll probably have to run new.
Life can only be understood backwards; but it must be lived forwards.
- Soren Kierkegaard