You can add the logic to the skin .ascx file in the OnLoad event.

Here is an example of what it would look like. 

<script runat="server">
    Protected Overrides Sub OnLoad(ByVal e As EventArgs)
        MyBase.OnLoad(e)
 
        If DotNetNuke.PortalSecurity.IsInRole("MyRole1") Then
            AttachCustomHeader("<link href='" + SkinPath + "css/my_layout-1.css' rel='stylesheet' type='text/css' />")
        Else
            AttachCustomHeader("<link href='" + SkinPath + "css/my_layout.css' rel='stylesheet' type='text/css' />") 
        End If

    End Sub

    Sub AttachExternalCSS(ByVal CSSPath As String)
        AttachCustomHeader("<link type='text/css' rel='stylesheet' href='" & CSSPath & "' />")
    End Sub
   
    Sub AttachExternalJS(ByVal JSPath As String)
        AttachCustomHeader("<script type='text/javascript' src='" & JSPath & "'></scr" & "ipt>")
    End Sub
   
    Sub AttachCustomHeader(ByVal CustomHeader As String)
        Dim HtmlHead As HtmlHead = Page.FindControl("Head")
        If Not (HtmlHead Is Nothing) Then
            HtmlHead.Controls.Add(New LiteralControl(CustomHeader))
        End If
    End Sub
</script>