It is very simple. The transducer has to have water contact to provide depth.
Those that have sonar units that have the imaging technology do attach those above the hull bottom, but use another transducer for depth.
If you state what sonar unit is involved and on what boat, you will get suggestions on the proper setup for it.
"One size does not fit all"
Humminbird Helix 12 SI, 1198c SI, 1198c SI, ONIX 10 SI NT, 360, RC-1