You need to expose it as a property to use it on the markup.
In the code-behind:
Private _useCss As Boolean
Public Property UseCss() As Boolean
    Get
        Return _useCss
    End Get
    Set(ByVal value As Boolean)
        _useCss = value
    End Set
End Property
Then in the markup:
    <%  If UseCss = True Then %>
    Your stylesheet link tag here
    <% Else %>
    else could be optional if you won't load anything
    <%  End If %>
Alternately you could have:
    <%  If UseCss = True Then
            Response.Write("text")
        Else
            Response.Write("something else")
        End If
    %>
Another option is to give your head tag an id and programmatically add the CSS file to it. To do this you don't need a property and could use the variable directly.
In your markup:
<head runat="server" id="head">
   <%-- whatever you typically place here --%>
</head>
In your code-behind, for example on page load:
Protected Sub Page_Load(ByVal sender As Object, ByVal e As System.EventArgs) Handles Me.Load
    If useCss Then
        Dim stylesheet As New HtmlGenericControl("link")
        stylesheet.Attributes.Add("rel", "stylesheet")
        stylesheet.Attributes.Add("type", "text/css")
        stylesheet.Attributes.Add("href", "../css/myCssFile.css")
        FindControl("head").Controls.Add(stylesheet)
    End If
End Sub