It is relatively easy to have 2 different databases that use the same version of RPP.
Do you really need to keep using version 2006 ? I am not aware of a good reason to keep with such an old version.
Alternatively, if Ver 2006 suits your purposes, is it possible to have 2 databases using version 2006 ? You could experiment with creating a second database in QPP 2006 and see how easy it is to open or switch between the different data sets.
I would expect the best solution is one version of QPP and two separate databases.
John