I don't know if you found an aswer as your question is a little bit old now.
But perhaps someone could find my answer useful.

I was also wondering how I can put in my process template my custom groups.
I tried a lot of things and I finally found it, exporting my widget with the OpenSocial Gadget.

In fact you can modify the xml file (Process Configuration Source) by adding a line which looks like :

<preference id="metagroups" value="Open~~New|Submitted@@Closed~~Closed"/>

In my usage, I wanted to group all the states New and Submitted (even if the workflows were different, so the states with the same name were different) and another group for Closed states.

So the complete result is :

<viewlet id="com.ibm.team.workitem.viewlet.statistics" trim="blue">
   <preference id="presentation" value="bar"/>
   <preference id="query" value="com.ibm.team.workitem.queries.predefined.planned_current"/>
   <preference id="metagroups" value="Open~~New|Submitted@@Closed~~Closed"/>
   <preference id="parameter" value="com.ibm.team.workitem.attribute.state"/>
   <preference id="othergroup" value="true"/>
</viewlet>

I hope this will help.