menu writer does not directly support creating different colors for each top level menu item, but it can be accomplished by editing the menu once created by Menu Writer.
you would need to add in line styles to each of the menu items to give them a unique color, for example, the menu item will look like:
<li><a href="index.php">Home</a></li>
add an inline background color to give a unique color:
<li><a href="index.php" style="background-color:#FF0000">Home</a></li>