Need some hepl with iTunes

[bxmedic]

Aside from my and my wife's phones we are a PC household. I am somewhat Mac illiterate.
I plugged my wife's phone in to add a ringtone and iTunes decided to delete the Playlists she had made on the phone & add a bunch of songs she had deleted. I have iTunes set to manually manage music. How do I make sure iTunes does not "fix" any changes that have been made on the phone? Is there a way to sync using the phone as the primary device?

Thanx