With 7.5+ GBs of email storage in Google Apps Education Edition, you will most likely not need to delete email messages to stay under storage quota. Keeping all your messages has advantages - you can keep and search for years of email - but with all of that storage, organization for your email is important to find messages quickly. Labels is a way to categorize all your email messages. Archiving is a way to organize your Inbox - the main view of Apps Mail.

You do not need to keep the thousands of messages in your Inbox to save them in your Apps Mail account. The "Archive" feature in Apps Mail can be used to move messages out of your Inbox and into your All Mail label, letting you tidy up your inbox without deleting anything. All Mail is your archive, a storage place for all the mail you've ever sent or received, but have not deleted. You can see a list of archived messages by clicking All Mail. Archived messages are also available by searching, and under any assigned labels. 

When someone responds to a message you've archived, the conversation containing that message will reappear in your inbox.

Deleting a message, on the other hand, moves a message into the Trash label. If you do not move the message out of trash for 30 days, Apps mail will automatically delete that message. Your message will not be available in All Mail, any labels you applied, or in search results. The email will no longer exist in any capacity. If you would like to find an email before it has been completely deleted, you can search for it using search operators or the advanced search options. Make sure to use the search query 'in:anywhere" when looking for mail in the trash.

Example:

Suppose you received an email message regarding an end of the year brunch. After reading the email once, you Archive the message because you don't need to read it again or have it sit in your inbox. A week before the event, you want to double check the event information. To do that, you click in All Mail and locate the message. Let's say 2 days later, the organizer sends out another email changing the date. That email will appear in your Inbox  in the conversation format, where you can see the original message and the new message in one view. Even though you archived the original message, the conversation reappears in your inbox because a new message came in. While archiving moves the message out of the main inbox view, you will not miss any new messages that are part of the conversation. 

Here's why we think archiving a message is better than deleting: