Maemo 6 looked to mainly be a progression of Maemo 5, so I'd assume that if you are using the same libraries for your application, it's likely it will work on both Maemo 5 and 6/MeeGo.
Look at most Linux distributions, Ubuntu 8 applications don't just stop working because Ubuntu 9 is out, aslong as the userland toolkits (gtk/qt) are up to date it should 'just work'.