LODs and Debris are glued as siblings to the top level LOD. (I use TrueView though, makes life MUCH easier

)
It should look something like this:
FreespaceModel
+-Lod0
..+-Main Hull
..+-local light
..+-Thruster01a
....+-thruster mesh
....+-local light
+-Detail1
..+-Main Hullb
..+-local light
..+-Thruster01b
....+-thruster meshb
....+-local light
+-debris01
..+-debris mesh1
..+-local light
etc.
Axis is set near the base and seems to scale it to that point - BUT it also moves it way back almost to the ship axis
Sorry, you lost me there, don't follow what you are trying to say it is doing. But... make sure that it is the mesh-light combination's axis that you are adjusting, NOT the actual thruster meshes' axis (which should be the center of the thruster mesh).
Insignia... I only know the old fashion way with a Hex Editor

Haven't tried to use Kaz's insignia tool in PCS yet. In general though... the area assigned for use by insignia MUST be triangulated. Also, think of the area defined as a "license plate" area upon which the "insignia stamp" will be placed by the FS2 graphics engine. This "plate" has its own set of vertices and its own UV space which must be defined. Also, you usually want the area define to be approximately square in shape so that there is no stretching of the insignia texture (which are 128x128). For an idea of how one is put together, open up one of the

fighter models with PCS and look at the insignia chuck
