BrightComet

If you have a look in the Settings menu I think there should be a place to log in.

I'm so oblivious. Thank you!
So now I'm logged in and I just wait?

Which section are you talking about? Can you screenshot it to show us?

After you've logged in on the program with your Neocodex details the next login should be your Neopets account.

Sure.

http://i50.tinypic.com/13zzybs.jpg

There you go.

Hold the title bar of the window (the Codex Checks window).

BTW: I need to get rid of one of your accounts by the way (you can't have two), so which one do you want to keep?

I guess I'll keep this one.
But still, when it says I need to log in again, what do I do?

Both of your accounts are validated. Can you try this:

It works, but then it asks me to log in again.
To here, or in the window?