You can create new melody voices using the voice utility which is in the right sidebar when the melody is selected. Information on how to use this is in the Hookpad user guide from the “help” menu.
Hookpad breaks up the midi files by instrument, so if you change the instrument on the same melody, it will create two separate midi files. When I work with my DAW, I find it most useful to export single instrument segments using the MIDI drag and drop feature, which Dennis talks about in this video:
Hope that helps!