If you're adding a wife and it finds a match and you use it, then yes, she'll be added as the wife but she won't automatially be set as the mother of the child. You have to go to the child and add the mother.
If you aren't on the Trusted List of a profile, you don't see the highlighted links that say "add mother" etc. You have to go to the Edit tab. You might want to contact the profile manager first though.