Yes, the CSS Navigation Menu will work with Frames. The frameID's will appear in the target dropdown field that is used to set the link for a menu item. Keep in mind, that this does not work for iFrames.
As a followup to my previous answer, I wanted you to know that we tested a few things. The menu can select frametargets, but the menu won't be visible ACROSS frames. The menu will only be shown in the frame where the menu code was placed.
Word of advise: Get rid of any frames-websites as they have to many drawbacks.