I use FTM2009 and in that, as with FTM2008, you can enter an alternate name for someone and then select the preferred name (probably the one they were know by most commonly), or you can enter an AKA for them.
I have both for my grandfather. I have his birth name Jules Jeffrey DEVOS, then his adopted name Edward REDSULL (set as preferred as he was known by this name) and then his commonly used name Ted as an AKA to his adopted name