Hi GrinGEO,
I suggest to export the geotiff in PhotoScan and then use qGIS (free & open source) to merge it with the geotiff of the Sonar data. Make sure that you have exported both datasets using the same coordinate reference system (CRS).
Here are the 2 functions that you will need to clip and merge the datasets in qGIS:
1 - Clip raster (i.e., geotiff): RASTER > EXTRACTION > CLIPPER
2 - Merge raster: RASTER > MISCELLANEOUS > MERGE
Alternatively, you could only work with your contour lines (shape files) and cut + merge them using qGIS as well.
VECTOR > GEOPROCESSING TOOLS
All the best.
Regards,
SAV