Whilst looking for a way to customize the "Custom" site templates name after create a Site Template, I came across the following this post which looks quite interesting. It shows you how to modify the Colloboration Portal to create your own Colloboration Portal Template
http://sharepointandstuff.blogspot.com/2007/07/customizing-out-of-box-collaboration.html
If you are looking for a way to fix the "Custom", the following post will help:
http://blogs.officezealot.com/mauro/archive/2007/06/13/20412.aspx
Apply a theme across all sites in a Site Collection
Also, if you want to apply the CSS of a particular theme across a whole site collection, or from a site and all its subsites, you'll need to do the following. You need to find the path to the theme you have chosen (e.g. /_themes/Lacquer/Lacq1011-65001.css), and then apply this to the top level site and all subsites in the Alternate CSS URL (Site Actions > Site Settings > Master Page). Once you apply the CSS to all subsites, you'll have gotten rid of the MS Blue forever ;)
Change the SharePoint Site Logo across a Site Collection
In case you want to change the Site Logo image across all the site collection, Shane explains cross how to easily do this using SharePoint Designer. Basically, you need to replace the Logo Place holder in the Site Collection master page with an img tag which references your logo.
- Browse to the top level of your site collection in the browser. Site Actions > View All Site Content. Select the Site Collection Images Library and upload your Company Logo (companylogo.gif)
- Open SharePoint Designer 2007 and Select File, Open Site. Type the URL of the top level of your site collection. Locate the master page gallery in the left pane. _catalogs\masterpage
- Double click the default.master (you may be prompted to check it out - if so choose yes)
- Search For: <sharepoint:sitelogoimage id="onetidHeadbnnr0" logoimageurl="/_layouts/images/titlegraphic.gif" runat="server/">
Repace With: <asp:Image runat="server" id="logo" ImageUrl="< %$ SPUrl: ~sitecollection/sitecollectionimages/companylogo.gif %>"/>
