Email forwarding and POP access are two separate tools that help you access your Yahoo! Mail from a different email account. Choose only one, whichever fits your needs better—they won't work at the same time.
With email forwarding, you'll automatically receive email addressed to your Yahoo! Mail account at your forwarding address. New email will not appear in your Yahoo! Mail Inbox while the forwarding feature is activated. Messages you received before you enabled email forwarding remain in your account.
POP access allows you to send and receive Yahoo! Mail using an email client (such as Netscape Mail, Outlook, or Eudora). If you select POP access, messages will appear in your Yahoo! Mail Inbox. Depending on how you configure your email client, you can either leave messages in your Yahoo! Mail Inbox or have them deleted when you download them elsewhere.
When you're using POP access, you can only retrieve email from your Inbox and Spam folder—the feature doesn't look for new mail in your other folders. So if you're checking your Yahoo! Mail from another account, you should delete any filters you might have set up that sort email to folders other than the Inbox.