I am able to seperate the look of front end and admin area side menu (they are shared by default) with the following code:
{if $usertype eq "C"}
<table cellspacing="1" width="100%" class="VertMenuBorder">
<tr>
<td>
<table cellspacing="0" cellpadding="0" width="100%"><tr>
<td>{$link_begin}<img src="{$ImagesDir}/{if $dingbats ne ''}{$dingbats}{else}spacer.gif{/if}" class="VertMenuTitleIcon" alt="{$menu_title|escape}" />{$link_end}</td>
<td width="100%">{if $link_href}<a href="{$link_href}">{/if}<font class>{$menu_title}</font>{if $link_href}</a>{/if}</td>
</tr></table>
</td>
</tr>
<tr>
<td>
<table cellpadding="{$cellpadding|default:"5"}" cellspacing="0" width="100%">
<tr><td>{$menu_content}<br /></td></tr>
</table>
</td></tr>
</table>
{else}
<table cellspacing="1" width="100%" class="VertMenuBorder">
<tr>
<td class="VertMenuTitle">
<table cellspacing="0" cellpadding="0" width="100%"><tr>
<td>{$link_begin}<img src="{$ImagesDir}/{if $dingbats ne ''}{$dingbats}{else}spacer.gif{/if}" class="VertMenuTitleIcon" alt="{$menu_title|escape}" />{$link_end}</td>
<td width="100%">{if $link_href}<a href="{$link_href}">{/if}<font class="VertMenuTitle">{$menu_title}</font>{if $link_href}</a>{/if}</td>
</tr></table>
</td>
</tr>
<tr>
<td class="VertMenuBox">
<table cellpadding="{$cellpadding|default:"5"}" cellspacing="0" width="100%">
<tr><td>{$menu_content}<br /></td></tr>
</table>
</td></tr>
</table>
{/if}
This is how I maintain the differences in look between admin and front end of the side menu that show category of product in my store. I am able to customize the side menu of front end without having to worry about it affecting the side menu in admin area. Is this how you guys do it too?