Most scanners will export the jaw model and the scanbody model separately but a new feature on the Medit upcoming software will let you export them as individual models or as a single merged model.
There are design advantages to both scenarios based on the practitioners skill level!
There are numerous ways to quickly check a model before taking it to a design software. Windows comes with at least 3 such free software. Another one to have handy is called 3dviewer.net to let you verify models really quickly