how to trace the checked out files?

If you're willing to do separate reports for individual object types, you can use the QueryBuilder function in Windchill to accomplish this (Site > Utilities > Report Management).  Here you can build a report on, say, EPMDocuments, to list all EPMDocuments in your system, their revision, iteration, and state, and only filter for those that are checked out.

Building these reports can be a bit tricky, as the interface is not the most intuitive tool.  I'd be glad to help and work with you and your company to implement this, or other reports or projects as well.  If you are interested, feel free to contact me directly at robert.sindelar@eccellent.com, or check out our website at www.eccellent.com.