When you have a Standard or a Premium mailbox, you can access it via POP3 or IMAP. These are two different protocols for downloading and accessing email.
If you choose POP3, you are downloading the email directly from the mail server into your email client, whether it is a desktop-based client or another webmail client. Your system stores a local copy of the email and deletes it from the server. You can create local folders on your computer to organise the email, but then when you log in using your webmail, you will not see the folders.
Because your email is being downloaded and deleted from the server, the only mail that counts against your mailbox limits are the ones left undownloaded in your inbox.
If you choose IMAP, you are downloading the email from the mail server into your email client, but you are also leaving it on the server. If you create folders on your computer to organise the email, you will also see these folders in your webmail. Also, when you mark a message as ‘Read’ in webmail, it appears ‘Read’ on your computer. This can be useful if you access your email on several devices.
But because your email is being left on the server, you will need to keep track of how much email you have and if you are close to your mailbox limit.