Once you have it, click on UE.jar then select the mod you want to add ships to (in the botf folder, you will find your installed mod (ie AAML, GALM, FLAG, UDM) click on the mod folder you want, then double click on the stbof.res)
once that's done, click on Edit, Click on Graphic and select Add/Remove Ships Models. A list of all the ships already in the mod will appear on the left window.
On the right hand side, click on Open Ship pack and select the location where you saved your ship packs.
Add the ships (by double clicking them) you want to one of the free slot on the left...note that in order to do that you need the scale and amount of phasers to be the same on both colums in order to be able to add them.
Once that's done, you click Edit, go down to Ships, select Ship Stats.....scroll the Empire you want the ships to be on....under the jpg, scroll to the filename.tga of the ship you want to add.
Once finished, you click on File, Save and overwrite the botf.exe when the popup appears.