I have done some testing on this with the latest version of CSS Menu Writer (2.0.3) in DW CS3 on Win XP. When I did this I can confirm that there is an editable region that is created for the menu_ie stuff, but I could not get it to create this area within the head editable region on my template. Please post back with some more info about the version of DW, the OS you are using and any other details you can think of about the process you used to apply the menu to the template.
I will do some more testing to see if there is an issue under certain circumstances that may cause this.
In my template the editable head region ends before any of the Menu Writer code begins.