By doing that you run the risk of having that overwritten if you perform an upgrade. Also if this is for the google tag manager, your script may not be in the right spot.
I got around this by creating a skin object that I placed in my skins that injects the tag manager code in the right spot. I can't remember where I originally found the code, but it could have been switzerland.
...
In the skinobject ascx
<%@ Control Language="C#" AutoEventWireup="false" %>
<script runat="server">
protected override void OnInit(EventArgs e)
{
base.OnInit(e);
var tp = (CDefault)Page;
tp.FindControl("Body").Controls.AddAt(0, new Literal() { Text = "<!-- Google Tag Manager --><noscript><iframe src='//www.googletagmanager.com/ns.html?id=TRACKING-ID'height='0' width='0' style='display:none;visibility:hidden'></iframe></noscript><script>(function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0], j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='//www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'scr" + "ipt','dataLayer','TRACKING-ID');</scr" + "ipt><!-- End Google Tag Manager -->" });
}
</script>