Roger, open this page: http://ancestry.custhelp.com/app/answers/detail/a_id/3669
This should explain what you need to do to split your family. If it doesn't come out the way you would like it, change the parameters to make it what you want. It does not affect your original file so no worries there. It creates a new file. Do it for your family and then for your wife's. If you want the files separate on Ancestry, do it before you upload the files.