The actual work flow isn't that difficult. Here is an L3 example:
1. Build the ship in DoGA L3 and export as a single 'part'.
2. Open Metasequoia LE and load in the ship as a part.
3. Use Meta to join verts and create/delete new polygons. You can select faces and hide them. This allows you to dig into a model and delete all the deadwood. This will reduce the size of the model, increase its display speed in the game, and stop z-buffer artifacts (zaggies.)
4. At this point you can export back to SUF, run the part through the L3 Object Convertor and do final textures in DoGA and export to X. However, there are some limitations that need to be observed. For example, many of the special effects in DoGA are actually render special effects and not .X model attributes. One trick is to make blended textures in DoGA, render them to a square and use that 'cooked' image custom texture.
Alternately, you can so all the texture and material creation in Meta. It's a little more work, but you have greater control on applying textures and such. And, you can also export to .X from Metasequoia LE as well.
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You can also use Milkshape 3D and other low polygon modellers in place of Metasequoia. There are pro and cons to each.
One of the details that I need to check out is multiple textures. DoGA, for example, uses textures as paint and applies an individual image tied directly to a given palette entry or material. This is perfectly legal in the .X format. If SE:SF uses a generic .X loader, you should be able to use DoGA based .X models just fine. If not, we'll need to be more creative on projecting textures to models.
Of course, there is more than one way to skin a cat. It should be know surprise that this alternate texture method is called skinning. :-)
The ship models in SE:SF are skinned. The advantage to skinning is that you can use a single image and map parts of it to specific polygons. The results can look good, but it is much more labor intensive then the 'paint and project' method. Milkshape 3D has a basic skinning tool that can be used. Many skinners use tools like Lithium Unwrap or its big brother Ultimate Unwrap.
It's possible to do 'skinning' with paint and project systems like DoGA, when you convert a part back into DoGA's SUF format, you can assign planar, cylindrical, or spherical texture mapping. So, you could make custom detailed texture and slap it right on top of a model.
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TAZ
(I'm sure this has been covered in the SE:SF mod threads, but I was on a roll.)
It looks like multiple textures are allowed. That will make life a lot easier for DoGA users.
A related SE:SF link... 
Re: Questions on SE V ship models
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