Here is a model to work with. The nodes Var1 and Var2 can be done in a similar fashion as the structure more likely than not but that is something for you to work on and if you run into issues post back with the code you tried.

Code:
Option Strict On
Module Module1
    Private MyList As New List(Of myStruct)
    Public Structure myStruct
        Dim Identifier As Integer
        Dim Array1 As Boolean()
        Dim Array2 As Boolean()
        Dim Number1 As Integer
        Dim Number2 As Integer
    End Structure
    Public Sub demo()
        Dim Struct1 As New myStruct
        Struct1.Identifier = 1
        Struct1.Array1 = {False, True, False}
        Struct1.Array2 = {True, True, True}
        Struct1.Number1 = 1
        Struct1.Number2 = 2

        MyList.Add(Struct1)

        Dim Struct2 As New myStruct
        Struct2.Identifier = 2
        Struct2.Array1 = {True}
        Struct2.Array2 = {True, True, True, False, False}
        Struct2.Number1 = 3
        Struct2.Number2 = 4

        MyList.Add(Struct2)

        Dim Result =
            <Config>
                <%= From T In MyList Select
                    <Struct>
                        <ID><%= T.Identifier %></ID>
                        <Array1><%= String.Join(",", T.Array1) %></Array1>
                        <Array2><%= String.Join(",", T.Array2) %></Array2>
                        <Number1><%= T.Number1 %></Number1>
                        <Number2><%= T.Number2 %></Number2>
                    </Struct> %>
            </Config>


        IO.File.WriteAllText(IO.Path.Combine(Application.StartupPath, "MyFile.xml"), Result.ToString)

    End Sub
End Module
The resulting file contents
Code:
<Config>
  <Struct>
    <ID>1</ID>
    <Array1>False,True,False</Array1>
    <Array2>True,True,True</Array2>
    <Number1>1</Number1>
    <Number2>2</Number2>
  </Struct>
  <Struct>
    <ID>2</ID>
    <Array1>True</Array1>
    <Array2>True,True,True,False,False</Array2>
    <Number1>3</Number1>
    <Number2>4</Number2>
  </Struct>
</Config>