The code that is produces by CSS Menu Writer by default will allow you to make edits to the menu. If it has been altered in some way that it is no longer recognizable by the tool you will not have these options.
If you have made edits to the code to cause it to break like this the only way to get it back is to undo the changes that you have made. The process for getting it working again will depend on the steps you took to alter it, since it works by default almost any alteration can cause it to no longer work like this.
If you have saved the menu as a new preset you can just remove the current implementation and apply it again. If you did not save the preset you should open up Menu Writer to see if the last custom menu is retained and if so save it as a preset so that you can just apply it to the page again.