In fact, you have two options:
1 to include it in the themes folder, and then the asp.net framework will automatically include it in all pages using this theme
2- to add a public variable to your CS code, which includes the path, and then use it in your code, as the following code:
public string basepath = "http://" + Request.Url.Authority + Request.ApplicationPath;
then use it in the ASP code:
<link type="text/css" rel="stylesheet" href="<%=basepath %>MyStyle.css" />
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