After initially creating a project and setting up your Project Properties to indicate copying of files into either a version or revision directory, as indicated in (Xilinx Solution 6704), you will notice that you do not see the appropriate files copied over in the first version/revision created within Design Manager.
This feature does not currently work on the first version/revision specified.
What you will notice in the directory structure is a "seedsrev.lst" in either the version or revision directory (depending upon if you choose version list or revision list). This file indicates the path to the file specified to be copied.
On subsequent revisions that are created, however, the seeds file feature does in fact work. This feature will be fixed in the next major release of our software.