You can set the quotas on the mail store database level on the mail server. In the Exchange System Manager expand the storage group you want to manage, right-click any mail store and go to the properties. Select the "limits" tab and set your quota limit there. It will affect all mailboxes in that mail store. You can set different quotas on every store if you want and move mailboxes into the store with the limit you want them to have.

You can set the quotas on the mail store database level on the mail server. In the Exchange System Manager expand the storage group you want to manage, right-click any mail store and go to the properties. Select the "limits" tab and set your quota limit there. It will affect all mailboxes in that mail store. You can set different quotas on every store if you want and move mailboxes into the store with the limit you want them to have.