Assuming you're using one of the later versions of Windchill, you need to create a condition in your publish rules based on document type.
<condition name="CAD_Drawing">
<attribute name="epmdoc_docType" value="Drawing"/>
</condition>
<condition name="CAD_Part">
<attribute name="epmdoc_docType" value="CAD Part"/>
</condition>
<condition name="CAD_Assembly">
<attribute name="epmdoc_docType" value="Assembly"/>
</condition>
<authoring-application name="PROE">
<if condition="CAD_Drawing">
...do stuff
</if>
<if condition="CAD_Part">
...do stuff
</if>
<if condition="CAD_Assembly">
...do stuff
</if>
</authoring-application>