From the database you now have, export GEDCOM files, select Partial: Exporting one GEDCOM file of the ancestors of your wife.Import that file into a new, empty database. Now Export a GEDCOM file of your ancestors from the original database, and import that into a seperate, new and empty database.
There will probably be a few people that don't get into either database, For these, choose to select the people to export To a GEDCOM,and select everyone. Deselect your ancestors and deselect your wife's ancestors, now export what's left and import that into a third new and empty database.
Now you have three databases.you can go through the odd people in the third database and put them where they belong by hand, or select them one at a time to export to another gedcom to be imported into whichever new database they belong in, you will have to link them to the proper people already in there. ( I didn't need this step, there were no strays left.)
Write me direct if there is anything you need help with.