Hi; I had a struggle with that too... here's what I had to do:
Run throught the default wizard.. then
1) Search Page: set the checked value either Y or 1
2) Results Page: Open up the search server behavior
3) Select the checkbox field and set the type to the database field type, set the checked & unchecked value properties to match the type and set the correct operators.
Hopefully that will do it. This was a huge learning curve for me and frankly I have not got my app to work because of other issues with the SQL.