Are you describing "mailboxes" in Apple's Mail app? That's odd, since this is the forum category for iPods.
The location of a new mailbox is determined by your Location selection when you created the new mailbox. In the panel that appears when you give command to create a new mailbox, there is a drop-down selection field for Location. Click that field. That is probably where you put your previous mailbox, so if the new one with the same name is duplicated at that location, that's the location you need to look.
If this question is about iPod (or iTunes), please post back with more details.