I need to use these conditional CSS files in my project too and I have done what you suggested below.
In my scenario, I have broken my CSS into formatting.css, nav.css and layout.css and these are being inluced when I run the site.
I then have a radmenu.css file in my themes folder which only works for skinning the RadMenu in Sitefinity.
My Ie6Fixes.css file (which I have included as you suggested) seems to load second in the list of CSS files at the time of loading.
Can you please have a look at my code and let me know if this is correct?
public partial class App_Master_Home : System.Web.UI.MasterPage
protected void Page_Load(object sender, EventArgs e)
//Check to see what kind of browser is requesting the page
HttpBrowserCapabilities Browser = Request.Browser;
//Attach a CSS style sheet accordingly
if (Browser.Type == "InternetExplorer6")
this.Page.RegisterClientScriptBlock("CSSLink", "<LINK href='App_Themes/Default/Css/ie6Fixes.css/ie6Fixes.css' type='text/css' rel='STYLESHEET' />");
this.Page.RegisterClientScriptBlock("CSSLink", "<LINK href='Style/IEStyle.css' type='text/css' rel='STYLESHEET' />");