Got a good reply from Chris in Customer Service:
"No need to uninstall Notion 5. You can use existing Notion 5 sounds - in Notion6, go to Preferences>Audio and then locate your existing sounds folder."
I also asked if we need the new v6 bundled sounds if we already own the whole Expansion set, and Chris' reply was:
"You may want to reinstall the keyboard bundle, as this contains the new organ, choir and harpischord sounds. By default this will install into Notion6 sounds folder, so you will want to move it once installed so all your sounds are in the same place."