Hi Stoorm!
You can use external DEM by using the tag in the coreg_ifg_computation.xml (or coreg_ifg_computation_subset.xml) named <externalDEMFile/> in the TopoPhaseRemoval and Back-Geocoding operators.
for using it you need to change :
<externalDEMFile/> by
<externalDEMFile>EXTERNALDEM_with_FULLPATH</externalDEMFile>
SNAP needs the external DEM to be a single GeoTIFF file.
In future releases of the snap2stamps it will be just as easy as introducing this in the configuration file project.conf, but for the moment you should do it manually as mentioned before.
I hope this helps!