As vapilot points out, you normally get the Mailbox size warning by email if you are in a corporate exchange environment. In that case, the quote counts everything stoed on the server, including your drafts, deleted items, sent items, and calendar.
It's always worth emptying those you don't need, especially deleted and sent items often hold many megs of useless data.
If you are running a POP3 account or IMAP, i.e. the typical home email account where you pull information from your server to your local computer, the settings can be found in Tools/email accounts.
hope this helps