You can base a Style on another Style and override specfic setters:
<Style x:Key="myStyle" TargetType="xctk:ColorPicker" BasedOn="{StaticResource {x:Type xctk:ColorPicker}}">
<!-- This will override the Background setter of the base style -->
<Setter Property="Background" Value="Red" />
</Style>
But you cannot “override” only a part of a ControlTemplate. Unfortunately you must then (re)define the entire template as a whole.