First you need to create them on the Custom Values tab on the workflow that you wanted them added to so they can be populated. Next on the Completion step settings, on the “Output IA value destination” you may select to step in the process where the UIMData values will be flattened into IA Values. For example, if I chose Completion as the destination for the flattened UimData / Field values, then after the Completion step is completed, you may examine the IA values for the fields values under the Completion step and will have he same name as the doc type fields. Lastly you would need to write some code somewhere to populate the Custom Values with the flattened values. Could do this in a .Net Code Module script or code behind script.
Hope this helps,