Hi,
If we assume that you have some additional software at disposal, I've got a few tips.
If your scatter data set is still too big for your model to handle, you can use either MatLab or e.g. ArcGIS (if you have access to it) to add elevation units to your mesh.
In ArcGIS:
If you create different shape layers which corresponds to your model extent, different zones etc, you can import these polygons into the mesh generator, either as boundaries straight away or as shape layers which you then use to draw your boundaries, zones etc. once again.
If you then create your mesh and export it, you'll have a mesh file with correct node values for X and Y but non-valid Z.
If you open your exported mesh in a text editor, copy all node coordinates and import to ArcGIS, and then use the Toolbox to assign a Z value straight from your DEM. Then export all points (with correct X,Y,Z now) to a text file, copy all values and paste them in your mesh file (replacing the X,Y,Z you copied the first time.
Now you'll have a working bathymetry file which you can use.
NOTE; If you have a very big project area, the abova operation in ArcGIS can take a lot of time. And you can't easily redo your mesh as you'll have to go through the steps above every time. Editing the bathymetry is fine though, you just can't change the position of the mesh nodes.
Hope it works out!
Best regards,
Jonas