I have finally figured out how to make Jquery work with any version of BlogEngine.  The best way to declare the scripts is in the .cs file of the masterpage of the theme that is being used.  Here is a sample code block to ensure that it will work.  Just place it in the Page Load method.

HtmlGenericControl js = new HtmlGenericControl("script");
js.Attributes["type"] = "text/javascript";
js.Attributes["src"] = Request.ApplicationPath + "/scripts/jquery.js";
Page.Header.Controls.Add(js);

HtmlGenericControl js2 = new HtmlGenericControl("script");
js2.Attributes["type"] = "text/javascript";
js2.InnerText = "$j = jQuery.noConflict();";
Page.Header.Controls.Add(js2);


Yeah,  I haven't tried it on version 1.6 and they say you don't need to use the noConflict method but at least the fist line will gauruntee it will work on any deployment.