On the Alert Settings page (Configuration > Alert Settings is displayed at the top), there is a 'tree' on the left hand side displaying your monitored entities (and groups if appropriate). Select the level that you which to configure for, e.g. a specific database. You will notice that the list of alerts changes so that only those alerts which apply for this level are displayed. Now when you select the alert any changes that you make will only affect the configuration for this level e.g. you can disable the alert for this specific database.
Here is some more information on configuration options:
http://www.red-gate.com/supportcenter/C ... 469820.htm