The easiest scenery design program for CFS2 is FS Scenery Creator. IMHO
http://fssc.avsim.net/Don't expect any 3rd party application to work in the same way as the M$ applications.
If these are proper CFS2 ships they aren't scenery at all. CFS2 ships are installed to the CFS2\SHIPS folder in the same way as aircraft. They're not selectable in Free Flight & can only be used in missions. They might need adding to mdlnames.txt & descrip.dat to show up in the MB. Full install instructions should be included.