There is a style that you can override (see below). The NavigatorWindow itself has no dependency properties that you could use to configure it so I don't think you can do more than restyling - but maybe thats all you need :-)
xmlns:avalonDockControls="clr-namespace:Xceed.Wpf.AvalonDock.Controls"
<Style x:Key="{x:Type avalonDockControls:NavigatorWindow}"
TargetType="{x:Type avalonDockControls:NavigatorWindow}">
<Setter Property="Background"
Value="{DynamicResource {x:Static SystemColors.ControlBrushKey}}" />
<Setter Property="SizeToContent"
Value="WidthAndHeight" />
<Setter Property="ResizeMode"
Value="NoResize" />
<Setter Property="shell:WindowChrome.WindowChrome">
<Setter.Value>
<shell:WindowChrome ResizeBorderThickness="10"
CaptionHeight="16"
CornerRadius="3,3,3,3"
GlassFrameThickness="4" />
</Setter.Value>
</Setter>
<Setter Property="Template">
<Setter.Value>
<ControlTemplate TargetType="{x:Type avalonDockControls:NavigatorWindow}">
<Grid>
<Border x:Name="WindowBorder"
BorderThickness="3"
Background="{DynamicResource {x:Static SystemColors.ControlBrushKey}}"
BorderBrush="{DynamicResource {x:Static SystemColors.ControlDarkBrushKey}}">
<Grid Margin="5">
<Grid.RowDefinitions>
<RowDefinition MinHeight="54" />
<RowDefinition Height="*" />
<RowDefinition MinHeight="42" />
</Grid.RowDefinitions>
<Grid>
<Grid.RowDefinitions>
<RowDefinition />
<RowDefinition />
</Grid.RowDefinitions>
<Grid>
<Grid.ColumnDefinitions>
<ColumnDefinition Width="Auto" />
<ColumnDefinition />
</Grid.ColumnDefinitions>
<Image Source="{Binding SelectedDocument.LayoutElement.IconSource, Converter={StaticResource NullToDoNothingConverter}}"
Stretch="None">
</Image>
<TextBlock x:Name="selectedElementTitle"
Text="{Binding SelectedDocument.LayoutElement.Title}"
TextTrimming="CharacterEllipsis"
Grid.Column="1"
VerticalAlignment="Center"
FontWeight="Bold"
Margin="4,0,0,0">
</TextBlock>
</Grid>
<TextBlock x:Name="selectedElementDescription"
Text="{Binding SelectedDocument.LayoutElement.Description}"
TextTrimming="CharacterEllipsis"
VerticalAlignment="Center">
</TextBlock>
</Grid>
<Grid Grid.Row="1">
<Grid.ColumnDefinitions>
<ColumnDefinition Width="Auto" />
<ColumnDefinition />
</Grid.ColumnDefinitions>
<Grid Margin="5">
<Grid.RowDefinitions>
<RowDefinition Height="Auto" />
<RowDefinition />
</Grid.RowDefinitions>
<TextBlock Text="Active Tool Windows"
FontWeight="Bold"
Margin="0,3,0,4">
</TextBlock>
<ListBox x:Name="PART_AnchorableListBox"
Grid.Row="1"
ItemsSource="{Binding Anchorables}"
SelectedItem="{Binding SelectedAnchorable, Mode=TwoWay}"
Background="Transparent"
BorderThickness="0"
MaxHeight="400"
FocusVisualStyle="{x:Null}">
<ListBox.ItemContainerStyle>
<Style TargetType="ListBoxItem">
<Setter Property="Cursor"
Value="Hand" />
<Style.Triggers>
<Trigger Property="IsMouseOver"
Value="True">
<Setter Property="Background"
Value="{DynamicResource {x:Static SystemColors.HighlightBrushKey}}" />
<Setter Property="TextElement.Foreground"
Value="{DynamicResource {x:Static SystemColors.HighlightTextBrushKey}}" />
</Trigger>
</Style.Triggers>
</Style>
</ListBox.ItemContainerStyle>
<ListBox.ItemTemplate>
<DataTemplate>
<Grid>
<Grid.ColumnDefinitions>
<ColumnDefinition Width="Auto" />
<ColumnDefinition />
</Grid.ColumnDefinitions>
<Image Source="{Binding LayoutElement.IconSource, Converter={StaticResource NullToDoNothingConverter}}"
Stretch="None">
</Image>
<TextBlock Text="{Binding LayoutElement.Title}"
TextTrimming="CharacterEllipsis"
Grid.Column="1"
Margin="4,2,0,2">
</TextBlock>
</Grid>
</DataTemplate>
</ListBox.ItemTemplate>
</ListBox>
</Grid>
<Grid Grid.Column="1"
Margin="5">
<Grid.RowDefinitions>
<RowDefinition Height="Auto" />
<RowDefinition />
</Grid.RowDefinitions>
<TextBlock Text="Active Files"
FontWeight="Bold"
Margin="0,3,0,4">
</TextBlock>
<ListBox x:Name="PART_DocumentListBox"
Grid.Row="1"
ItemsSource="{Binding Documents}"
SelectedItem="{Binding SelectedDocument, Mode=TwoWay}"
Background="Transparent"
BorderThickness="0"
MaxHeight="400"
FocusVisualStyle="{x:Null}">
<ListBox.ItemContainerStyle>
<Style TargetType="ListBoxItem">
<Setter Property="Cursor"
Value="Hand" />
<Style.Triggers>
<Trigger Property="IsMouseOver"
Value="True">
<Setter Property="Background"
Value="{DynamicResource {x:Static SystemColors.HighlightBrushKey}}" />
<Setter Property="TextElement.Foreground"
Value="{DynamicResource {x:Static SystemColors.HighlightTextBrushKey}}" />
</Trigger>
</Style.Triggers>
</Style>
</ListBox.ItemContainerStyle>
<ListBox.ItemTemplate>
<DataTemplate>
<Grid>
<Grid.ColumnDefinitions>
<ColumnDefinition Width="Auto" />
<ColumnDefinition />
</Grid.ColumnDefinitions>
<Image Source="{Binding LayoutElement.IconSource, Converter={StaticResource NullToDoNothingConverter}}"
Stretch="None">
</Image>
<TextBlock Text="{Binding LayoutElement.Title}"
TextTrimming="CharacterEllipsis"
Grid.Column="1"
Margin="4,2,0,2">
</TextBlock>
</Grid>
</DataTemplate>
</ListBox.ItemTemplate>
<ListBox.ItemsPanel>
<ItemsPanelTemplate>
<WrapPanel Orientation="Vertical" />
</ItemsPanelTemplate>
</ListBox.ItemsPanel>
</ListBox>
</Grid>
</Grid>
<Grid Grid.Row="2">
<TextBlock Text="{Binding SelectedDocument.LayoutElement.ToolTip}"
VerticalAlignment="Center">
</TextBlock>
</Grid>
</Grid>
</Border>
</Grid>
<ControlTemplate.Triggers>
<Trigger Property="SelectedDocument"
Value="{x:Null}">
<Setter Property="Text"
Value="{Binding SelectedAnchorable.LayoutElement.Title}"
TargetName="selectedElementTitle" />
<Setter Property="Text"
Value="{x:Null}"
TargetName="selectedElementDescription" />
</Trigger>
</ControlTemplate.Triggers>
</ControlTemplate>
</Setter.Value>
</Setter>
