The PlayOnline Viewer installs first. Use the POL code for that. You can't miss it when it asks you for it. More than an hour later (after you install the updates and crap), you can install FF11. It'll ask you for the FF11 code. It's hard to miss, too. Use the right code for each.
If neither of your codes work, get another set of codes just like you did the first time. My codes worked fine when I entered them so I don't know if you'll need another email address to get another set of codes. Good luck.
Edit: It's tedious as hell, especially with a controller. If I had a USB adapter for my PS/2 keyboard, I would have used that to enter my info. Yeah, yeah, I'm livin' in the Stone Age.