I fully customized mine. Mine lays out on the same page. The results just push everything down. That style is not in an iframe. I used firebug to tell me everything I needed to know about what to target.
The previous page discussed how you can use the control panel to customize the look and feel of your search box and search results. This page discusses how you can implement the customization using the context file, which is the XML specification for your search engine.
What you’re doing now is basic customization which you can change in the options area. Are you using GSE through adsense or not? I use it through adsense and I have those options.