[Drake113]

No, it's sorta supposed to look that way initially. You don't even want to know how scary the Andromeda Ascendant was when I started this endeavor; that's the reason I shelved the Andromeda mod right off the bat and went for Battlestar Galactica instead.
Ok, you should have a menu bar down the right side with the following stuff:
+ Groups
+ Materials
Bones

Click on the + next to Groups. Then, right click on the first group, click "Select", then Edit>Scale>Arbitrary>.5x>Close. This will scale down the selected group to half size. Now, move it somewhere out of the way, right click the group again, and click "Unselect". Repeat for the rest of the Groups.
Ok, now that you've scaled down your respective Groups, the next trick is to get them all to coexist in that gray box without overlapping. Ideally, you want to make them as big as possible so you'll get the most amount of detail out of your texture.
Now, delete all the stuff under materials and save it as an XFile. Now click File>UV Map>Save and name it something like miranda.bmp. This is BMP of a wireframe representation of your ship, and this is what you'll be applying your textures to in your trusty image editor. Open it along with the other BMP files in the that directory (for the Miranda, it's the FCL directory and you'll want to open FCL_1_1.bmp, FCL_1_2.bmp, FCL_1_3.bmp, and FCL_1_4.bmp. you can ignore the rest as they are all either damage maps, light maps, or lower resolution). Now scale those BMPs so they fit over the proper parts of your UV Map (miranda.bmp). Once you're convinced it looks OK, scale the UV Map to 256 x 256 and open up your Xfile in Lithunwrap again.
Now, click Materials, rename it Miranda.bmp, and right click, then properties. Under Diffuse Map, select BMP, then Properties>Change>miranda.bmp. Now at the top, click Preview>Show Model. You may have to go back and forth between Lithunwrap and your image editor; I find it's easiest to keep them both open and just click reload under the same properties menu that you initially loaded the material to in the first place.

With any luck, that should get you on your way. I know it seems like a lot, but once you know your way around, you can probably kick out a pretty good looking model in under an hour. And good choice with the Miranda-- that's one of my all time favorite Trek ships.

Take care,

Drake