You should view my previous answer Mailbox notifications in which I discuss mailbox quotas in a bit of depth.
Once you review this, you can set mailbox quotas either at the store level or the mailbox level. To set quotas across an entire store, navigate to the properties page for the store of interest in Exchange Administrator. Then, on the General tab, set the Issue warning, Prohibit send and/or Prohibit send and receive based on what you learned from my discussion of quotas.
Alternatively, if you just want quotas set on a mailbox-by-mailbox basis, you can view the properties of a mailbox in Exchange Administrator, navigate to the limits tab, and set the quotas there.
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