Well, it ain't morning (unless, of course, you consider anything beyond midnight to be morning), but I'm here anyway
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Eder explained it pretty well already, actually. You gotta use TREMAN to extract everything from the ueships1/2/3.tre files (1 and 2 are capships and fighters, not necessarily in that order, while 3 contains other ships that are used mainly in cutscenes). If you want to mess around with these ships in UE (rather than SO), you also have to edit the ue_tre.cfg file. Just put some random characters in front of the first line (install no_folders 0), so that the DLL doesn't recognise it.
As for using them in SO... replacing SO ships is as simple as renaming the UE ship files, so that the game reads them instead of the SO ships. So, if you wanted to try playing SO with everybody's favourite Scimitar instead of the Panther, you'd rename the file ships\scim.iff to panthrbl.iff (or panthblb.iff, or panthblf.iff - these are other SO variants of the Panther). Note that, as Eder already said, you'd have some gun trouble with UE ships in SO. The Scim is one exception - it would have dust cannons instead of vipers, which isn't really too much of a difference.
Note also that replacing the Cerberus (or, in WCP, the Midway) with the Dauntless or any other UE ship will cause problems, because these ships are not designed to use the automatic takeoff/landing sequences in WCP/SO, and may cause the game to crash during takeoff.
And now, I shall go to sleep
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