I've managed to do the upgrade the Ms Search Server 2008 Express in conjuction with WSS 3 SP1.
According to the http://technet.microsoft.com/en-us/library/cc297193.aspx - "Configure site collections to use the Search Center" section, I think I am missing the procedure to use this.
It said that I need to have different URL (See: 4.Type the address of your Search Center in the text box, for example, http://servername:port.)
So what did I miss here? At the moment, my search seems ok but I don't think I am using the right interface.
Any ideas?