If you want to know the depth under the keel, you do not need the distance from waterline to transducer. Offset can be positive, negative or zero. In your case, for depth under the keel, you need a negative offset (keel's depth).
One quick way to go about it is to use some drawings from owner's manual and match up a known distance (waterline, boat LOA, draft, etc. ) as a reference and measure the distance you want. It's not perfect but i would say it falls within 10 cm range or less.