What versions of Menu Writer and DW are you using and what is your OS? Also what is the page type of your template file? You should always be able to edit an existing menu that you put on a page from the property inspector.
If the menu is static you can make edits to it directly on the page but any time that you edit the menu outside of the interface you can loose the ability to edit within the interface or have your changes reverted if you edit within the interface afterwards.
Can you post a copy of the template file in question and include a copy of your CSSMW folder in a zip archive? We can take a look at it for you.