The only way to have a menu in the top frame show correctly would be to use java script to show the menu items in the bottom frame. this is not something that is supported by menu writer.
Menu Writer will not be able to work in your frames design in this way.
Are you using frames as a means to have the same menu on each page or is there another design reason for using frames?
If the choice of using frames is to create one page to manage the menu, you should consider using a Dreamweaver Template instead.
Add the menu to the template and the menu will be added to each page derived from the template.