If you're making ships for use in FS_open, I wouldn't bother. The new flares are much better looking, and all you have to do is add an engine glowpoint.
Otherwise, the thruster cone is just a subobject with a texture called 'thruster01' (i.e. a BMP - the game automatically substitutes in the correct ani texture for that ships tbled species). There is not restriction upon the actual shape of it.
The thrust flame is scaled along that objects Z-axis - the centre-point of the axis is where the flame starts from.
Each LOD needs a thruster subobject. i.e. LOD0 is thruster01a, LOD1 thruster01b. You can have multiple 'thrusterxx' objects (i.e. thruster02a, thruster02b, etc)
