I'm using GeekLog 1.8.2sr1 and I had the same issue with the 'default'-(Clunky?)-Menu.
I've done some Hacking. The one thing I used to where I have FULLer-Control of the MENU is to utilize the "Menu Plugin (beta version)" found in France -
It took me about 2-Days to figure out how to Custom-Configure the Menu-Beta since there doesn't appear to be any instructions written for it BUT once you get a hang for creating the Sub-Menu ... it's Functional-Fast-n-Pretty!
AFTER I got the Menu-Beta working ... I made a modification to the the header.thtml FILE found in the layouts template folder (I'm using a modified-copy of the default "professional" template) and Eliminated the default menu in this following Code:
Text Formatted Code
<div class="header-navigation-container clearfix">
<!-- <ul> -->
<!-- menu_elements plg_menu_elements - both Sets-of-Braces removed WTT -->
<!-- </ul> -->
</div>
Hope this helps.