You can create a theme to use across your application. There are a couple of themes available in the AvalonDock distribution that can be used as an example or template to create your own (e.g. VS2010 theme).
You then just apply it to your DockingManager:
<dock:DockingManager x:Name="dockingManager"
AnchorablesSource="{Binding DockModel.Tools}"
DocumentsSource="{Binding DockModel.Documents}"
ActiveContent="{Binding DockModel.ActiveContent, Mode=TwoWay}">
<dock:DockingManager.Theme>
<adCustom:DarkBlossomTheme />
</dock:DockingManager.Theme>
<dock:LayoutRoot/>
</dock:DockingManager>