To select or clear a field type of "checkbox" in Pardot, reference the field with fieldname and underscore 0 .  To clear a  checkbox set  fieldname to an empty string,  and to select it set it to the name of the field. 

For Example

In this example, your custom field is called customfield and your check box is called Testbox.

To select it, use  {"customfield_0":"Testbox"}.

To clear it, use {"customfield_0":""}.