ListBoxItem doesn't have a "click" event, so it is not clear what you were doing or what functionality you lost when you added the ControlTemplate.
If you have a button in your ControlTemplate you can set its Click event exactly the same way as you would outside the ContolTemplate. Here's a simple example where ListBoxItem does nothing other than show a Button beside the content, and that button calls an event handler named "OnClickMeButtonClicked":
<Style TargetType="ListBoxItem">
<Setter Property="Template">
<Setter.Value>
<ControlTemplate TargetType="ListBoxItem">
<DockPanel>
<Button Content="ClickMe" Click="OnClickMeButtonClicked" />
<ContentPresenter />
</DockPanel>
</ControlTemplate>
</Setter.Value>
</Setter>
</Style>
If what you meant is you want your ListBoxItem to display differently depending on whether the item is selected or not, just set a trigger on IsSelected:
<ControlTemplate TargetType="ListBoxItem">
<Border Name="Bd">
<ContentPresenter />
</Border>
<ControlTemplate.Triggers>
<Trigger Property="IsSelected" Value="true">
<Setter TargetName="Bd" Property="Background" Value="Blue" />
</Trigger>
</ControlTemplate.Triggers>
</ControlTemplate>