Hi Yukai,
you can set the sub folder by adding it to the file name of your template like this:
If you have an allrun script which you execute for each design this would normally be executed in the same location as your STL file is exported to. Hence, typically referring to it by its name instead of full path works. Alternatively, you could add an entry an specify a path with getResultsDir() to have it adjust dynamically...
Cheers,
Heinrich