Hi Anthony,
Once the xml upload is done, comparsion indexes should be generated and updated.
In the selection screen you have an option of processing mode- where you can setup if you need generation of comparison index to happen at the time of upload.
If you have this done, then there is no need of a separate step.
But advisable process is to first complete the upload and then have a separate step of generating comparison indexes. We actually have a separate batch job setup for generation of comparison indexes. This would be the best way rather doing it in one go.
For your reference: http://help.sap.com/saphelp_gts70/helpdata/en/b4/140e2258cb214c8a45825fc266e228/content.htm
Regards
Dhilipan