Importing the XTF file: Must use the correct file importation option:

Vessel Geometry: If the system was a towed sonar, to get a DTM that represents the total water depth use the "Tow Fish or ROV System Configuration:

All Benthos C3D systems should have a pressure sensor that allows computation of the towfish depth, so "Add Depth from XTF" is checked by default. The other offsets will be small (<1m) because all the components are mounted inside the towfish.
In the case of a pole mounted (LPM) system the offsets will be more typically like those of a conventional multi beam sonar. See the detailed explanation in the Vessel Geometry description.
Bathy Processing: In the Bathy Processing > Select processing dialog choose the Navigation Packet (42) option and the Gyro Packet (84) option to use high speed navigation and gyro packets for better positioning and heading:

It is possible that the XTF file you are processing may not contain these packet types - then if you choose these options you will get a warning that there is "No Navigation" in the file during processing, go back and choose one of the other options.
Attitude Correction Settings: In the Attitude Correction Settings you MUST check the box "Use C3D precise timing (Benthos C3D only"

This setting ensures that the Triton/Benthos Precise Timing Architecture is used in the attitude processing, There is a special Epoch Time {E} tag added to the attitude datagrams that come from the Benthos C3D that are logged by Isis MB/SS-Logger and used by BathyPro that greatly improve the attitude correction with this sonar type.