4
           
            
                
     
    
    Another way that you can modify the main menu and not affect the way that it does its magic is by modifying the template for it in the XOOPS Admin->System Admin->Templates manager. This template should be under the systems module. This way it will show up the same way under every theme that you have available. 
system_block_mainmenu.html is the template that you will need to edit. Just look at the code to match up the css styles and you should be fine. I had to do this to add in a couple custom links to the user block. 
 <table width="100%" cellspacing="0"> 
  <tr> 
    <td id="mainmenu"> 
      <a class="menuTop" href="<{$xoops_url}>/"><{$block.lang_home}>a> 
       
      <{foreach item=module from=$block.modules}> 
      <a class="menuMain" href="<{$xoops_url}>/modules/<{$module.directory}>/"><{$module.name}>a> 
        <{foreach item=sublink from=$module.sublinks}> 
          <a class="menuSub" href="<{$sublink.url}>"><{$sublink.name}>a> 
        <{/foreach}> 
      <{/foreach}> 
       
    td> 
  tr> 
table>  
I supplied the original code for the main menu. Just add in your custom links after the last closing tag for the row.
 <table width="100%" cellspacing="0"> 
  <tr> 
    <td id="mainmenu"> 
      <a class="menuTop" href="<{$xoops_url}>/"><{$block.lang_home}>a> 
       
      <{foreach item=module from=$block.modules}> 
      <a class="menuMain" href="<{$xoops_url}>/modules/<{$module.directory}>/"><{$module.name}>a> 
        <{foreach item=sublink from=$module.sublinks}> 
          <a class="menuSub" href="<{$sublink.url}>"><{$sublink.name}>a> 
        <{/foreach}> 
      <{/foreach}> 
       
    td> 
  tr> 
<tr> 
<td> 
<a href="<{$xoops_url}>/customlinklocation">custom linka> 
td> 
tr> 
table>  
If you do that you should be good to go with custom links in your main menu.