You are aware that flash is not within the specs by now right?
Anyway, this Sigil you are not able to edit the opf. At least, not in this version. You can add the swf file however by clicking on the misc folder on the left and add existing item.
You must edit the epub by hand to edit the opf. An epub is essentially a zip file, packed/created in a specific way. You can use for example tweak_epub
for it. Open the epub with the program, select the opf and press edit. Make your changes and save.
I recommend reading through the Jedisaber tutorial
on creating ePub by hand to get the feeling on what an ePub is and how it is build.