If the query contains applicable criteria, it will be added to the corresponding Summary field automatically if Yes is selected.  

For example, if a Constituent query has criteria
Gift Date between 1/1/2005 and 12/31/2007

Then a Summary Field is selected for Total Amount of Gifts.  Set the operator to greater than or equal to 1
Switch to the Filter tab and the Gift Date between 1/1/2005 and 12/31/2007 will be added as a filter already.

This ONLY applies to criteria that would be applicable for the Summary field.  So gift criteria would be added to a Summary for Gift, but Actions criteria would apply to Summary for Actions.

This option is an individual user option.  It can be turned off by doing the following:
1. Go to Tools>User Options
2. Select the Query tab
3. Select Advanced on the left
4. Change the selection to "Do not automatically apply all query criteria" from Ask me each time I select a summary field