I struggled with this problem in C14, too!
Different sample librarys use different octaves, so that the MIDI notes that have to be used don´t show up in the right octave in notation. Instrument types and clefs are too limited to have the notes show up in the correct octave.
Was no problem in the old score editor, where you could transpose each staff any way you wanted it…
Wrote about this problem in a different thread already: