You copy one of the the ship model's lods, rename it "shipname"_COL.lod, and add the pertinent line to the ship's data ini file.
For example, say you have a 3rd party Grisha-class corvette. You would copy one of it's lod files (usually the lowest poly one), rename it Grisha_COL.lod, and then in the Grisha_Data.ini, you perform the following edits (examples in bold type):
[GroundObjectData]
DamagedModel=
DestroyedModel=
DestroyedEffect=ShipDestroyedEffect
DamageEffect=ShipFireEffect
SystemDamageEffect=ShipSystemFireEffect
CollisionMesh=Grisha_COL.LOD
SinkTime=60.0
EmptyMass=6000000.0
Save your edits, and you should be good to go.