When you add your email account to a phone, most mail apps ask you to choose between IMAP and POP3. The choice affects whether your inbox looks the same everywhere you check it, or whether each device holds its own separate copy of your mail.
How IMAP works
IMAP keeps your mail on the server and shows your phone a live view of it. When you read, delete, or file a message on your phone, that same change shows up on your laptop, your webmail, and any other device connected to the same account. Folders you create also sync across devices.
How POP3 works
POP3 downloads messages to whichever device checks the mailbox first, and by default removes them from the server afterward. If you read a message on your phone with POP3, it may not show up at all when you later open webmail or check the account on a computer, because the server no longer has a copy.
Which to choose
For a phone, choose IMAP in almost every case. Business email is rarely checked from only one device, and IMAP is what keeps read status, folders, and sent mail consistent everywhere. POP3 still has a narrow use: a single archival device that is meant to store a permanent local copy of everything and does not need to match what other devices show.
Storage on the server
Because IMAP keeps everything on the server, your mailbox will fill up faster than it would with POP3, since nothing gets automatically removed after download. Check your mailbox quota periodically in your control panel's Email Accounts section, and clear out old Sent Items and large attachments if you are approaching your limit.
If you have already set up an account as POP3 and want to switch, the cleanest way is to remove the account from your phone and add it again, choosing IMAP this time. There is no in-app option to convert an existing POP3 account to IMAP.
Whichever protocol you use, the actual server address and ports you enter come from your control panel's mail client configuration page, and these do not change based on which protocol you pick, only the port number differs between the two.