The waterline has nothing to do with it unless you have a displacement hull, not a planing hull.
(You do mean HULL, don't you?)
For a puck (flat) transducer, you normally mount the lead end flush with the boat bottom, and then tilt the aft end downward about a degree or 2. That way the ducer makes firm contact with the water.
If you have a torpedo type ducer (like maybe a chirp) its normally mounted with the circumference slightly below the bottom. They usually provide a fairly good rooster tail, but work well at high speed..
If you don't care about high speed accuracy, you can mount it anywhere.
We don't know what you have. If you look online you can download the installation manual for your specific model. Mounting on a tube is the same. Consider the lowest (rounded) portion of the tube to be the bottom of the boat, and then follow the directions as indicated for a traditional hull.
Been there, done that. Expect a rooster tail because its a tube not a "hull".