I'm not sure about the specifics in the Apple ecosystem but I imagine it's like an email address that's connected as IMAP on one main PC, and as POP3 on your phone.
You can download the mails you need to your phone to read them and answer them on the go.
But the mail server is synched to the PC. So deleting stuff on your phone just deletes the messages on your phone, not on the server and not on the PC.