Hi Andria,
The settings in the Html will only affect the slideshow if used in the Html instance it will not affect your header slide show, I just pointed you there for the help documentation. All the Html feature is doing with those settings is using them to determine what properties to set on the <portal:SlidePanel inside the Html feature.
You can specify settings directly on the control like this:
<portal:SlidePanel id="spanel1" runat="server" CssClass="rotatecontainer" TransitionEffect="fade,curtainX,turnUp,slideY,zoom,pinch,scrollRight" Random="true" TransitionInterval="3000" Speed="1000">
</portal:SlidePanel>
The properties I've shown here are the ones of interest, by default the TransitionEffect is only fade, but you can specify them comma separated as shown above, and the help in the html feature lists the possible transitions.
Best,
Joe