People are always asking me for information about how they query Sharepoint Portal Server Search.  This article shows the 3 simple ways to do this.  Just the basics ... but a good starting point.

http://www.msdn.microsoft.com/office/understanding/sharepoint/default.aspx?pull=/library/en-us/odc_sp2003_ta/html/office_sharepointportalserversearchbox.asp

Also links off to reference doco etc...