This is of course the horrible issue with pro-portal - it is very hard to customise - everything is GLOBAL.
What you could try -
no guarantee it will work - is to add a pro-portal template set to the theme you are using and to edit that.
you should be able to go to the theme templates and ADD a template - try adding the pro_portal templates (there are 5 I think - in global templates) to the theme set.
Then, edit one of the templates with a single word - Like Potato or cabbage - and see if it shows.
Example code:
[html]
<html>
<head>
<title>{$mybb->settings['bbname']}</title>
{$headerinclude}
</head>
<body>
{$header}
<table width="100%" cellspacing="0" cellpadding="0" border="0" align="center">
<tr>
<td valign="top" width="{$proportal->settings['leftcolwidth']}" style="padding-right:{$proportal->settings['verticalspace']}px">
{$leftblocks}{$rightblocks}
</td>
<td valign="top">
{$centerblocks}
</td>
</tr>
</table>
<table width="100%" cellspacing="0" cellpadding="0" border="0" align="center">
<tr>
<td align="center" width="100%" class="smalltext"><a href="http://www.promybb.com/" target="_blank">Pro Portal 1.0</a> © 2010 <a href="http://atopal.com/" target="_blank">Adnan TOPAL</a></td>
</tr>
</table>
{$footer}
</body>
</html>
[/html]
I just tested it on testfish and it works - see the greenfish portal vs the bluefish portal.
Now I just have to fix the PM section! Could I put width auto in javascript?