At this stage sets of design files which can be ordered together must be created during the 'Add a new design' stage of the process.

You'll need to upload your multiple design files together in a batch here:
http://www.ponoko.com/design-documents/add
Use the 'Add another design' option after your first begins to upload.

Once you've got all the files uploaded, click 'Done', add materials to all of your files and then you can order them together.

You can read more about this here:
http://support.ponoko.com/entries/491380-pricing-designs-and-choosi...

I hope that helps!