If the system finds an old serial number, it won't ask you for it again. That's why most people only have to enter the upgrade number.
If you install on a fresh system, you enter your Logic 9 serial number. If this is an upgrade number, you will need to enter a serial number for an older full (non-NFR, non-Education) version of Logic! This can be an XSKey with a full license of e.g. Logic Pro 7, but _not_ an upgrade serial number to Logic 8. Older upgrade number become useless if you want to upgrade to the latest version.