The following method would be called after a form submit occurs on the popup. I placed the method call in the OnClick event for my submit button. The preprocessor directive of System.Text is required for the stringbuilder that I use below (You don't actually have to use a stringbuilder, but I find it makes it easier to read and debug later).
private void RegisterCloseWindowScript()
{
if (!Page.IsClientScriptBlockRegistered("CloseWindow"))
{
StringBuilder sb = new StringBuilder();
sb.Append("<script language='javascript'>");
sb.Append("window.opener.location.href = ");
sb.Append("window.opener.location.href;");
sb.Append("window.opener.focus();");
sb.Append("window.close();");
sb.Append("</script>");
Page.RegisterClientScriptBlock("CloseWindow", sb.ToString());
}
}