To change navigation pane colors you need to access the navigationPane.NavigationBar.ColorScheme object.

C#:

private void Form1_Load(object sender, EventArgs e)
{
    ColorScheme colorScheme = navigationPane1.NavigationBar.ColorScheme;
    // Office 2007, 2010 and Windows 7 styles use global color scheme
    // Note that changes to global color scheme affect all controls that use changed colors
    if (navigationPane1.Style == eDotNetBarStyle.StyleManagerControlled ||
        navigationPane1.Style == eDotNetBarStyle.Office2007 ||
        navigationPane1.Style == eDotNetBarStyle.Office2010 ||
        navigationPane1.Style == eDotNetBarStyle.Windows7)
    {
        Office2007ColorTable colorTable = ((Office2007Renderer)GlobalManager.Renderer).ColorTable;
        colorScheme = colorTable.LegacyColors;
 
        // This is default background color for unselected items
        colorTable.NavigationPane.ButtonBackground = new GradientColorTable(Color.White.ToArgb(), Color.DarkGray.ToArgb());
    }
 
    colorScheme.PanelBackground = Color.Red;
    colorScheme.PanelBackground2 = Color.DarkRed;
}

VB:

Private Sub Form1_Load(ByVal sender As Object, ByVal e As EventArgs)
    Dim colorScheme As ColorScheme = navigationPane1.NavigationBar.ColorScheme
    ' Office 2007, 2010 and Windows 7 styles use global color scheme
    ' Note that changes to global color scheme affect all controls that use changed colors
    If navigationPane1.Style = eDotNetBarStyle.StyleManagerControlled OrElse navigationPane1.Style = eDotNetBarStyle.Office2007 OrElse navigationPane1.Style = eDotNetBarStyle.Office2010 OrElse navigationPane1.Style = eDotNetBarStyle.Windows7 Then
        Dim colorTable As Office2007ColorTable = DirectCast(GlobalManager.Renderer, Office2007Renderer).ColorTable
        colorScheme = colorTable.LegacyColors
 
        ' This is default background color for unselected items
        colorTable.NavigationPane.ButtonBackground = New GradientColorTable(Color.White.ToArgb(), Color.DarkGray.ToArgb())
    End If
 
    colorScheme.PanelBackground = Color.Red
    colorScheme.PanelBackground2 = Color.DarkRed
End Sub