Hopefully my dear friend and colleague Peter won't mind my amplifying his question a bit. It occurs to me that because you are confused with where the Home link is heading, that you might also question what is meant by his question about what is set as the default.
When you double-click the WebHelp layout in the Single Source Layouts pod, or when you click File > Generate > WebHelp from the menu, you end up seeing the properties for the layout. From that dialog, if you expand the Content Categories and click the default category, you see options that govern the way that layout will be generated. One of the options is named "Default Topic". It is this option Peter is referring to.
Note that you may need to click the Select button and nominate a different topic here.
Peter and Captiv8r,
Thank you very much for your help. That fixed the problem.