You can use "PartDocReference~create~wt.part.LoadPart.createPartDocReference" loader to create part document relationship in bulk. you can create CSV file for attaching one document to Multiple part and then load csv file to in to windchill after converting it into xml. Attached is sample csv and xml file of loader. refer data loading guide(http://www.ptc.com/WCMS/files/156986/en/WCDataLoadGuide.pdf) for more details
Hope this helps !!!
Thanks
Shreyas