In principle you can use any reference level in the hydrodynamic computations (that is in the bathymetry), but it is recommended to use mean sea level (MSL).
The depths on sea charts are, however, normally given relative to the lowest astronomical tide (LAT) and the bathymetry will therefore normally be entered (digitised) relative to this datum. You can add the difference between MSL and LAT to all grid points in the bathymetry data file using the Grid Editor facility for editing.
You will have to make sure that all the sea charts you are using to prepare the bathymetry are relative to the same datum. If this is not the case, you must choose a common datum and then convert all depths to this datum. In the same way, all the water level recordings you will use must also be converted to the same datum.