Hi Tys,
I might be misunderstanding this but If you define your schema elements with a minOccurs="0" attribute then generally the elements will be omitted from the resulting XML. So something like;
<xs:element name="Field1" type="xs:string" minOccurs="0" />
A checkbox seems to be a bit different as by default it has values of 1 for on and 0 for off (so is never empty). To get an xml element bound to a checkbox to be omitted from the resulting xml you seem to have to change the off value to an empty string, in the Object Binding tab.
Bruce