Thanks Edgar and Frank. The following worked in the end.
Flaps unregisterQuadsWithReceiver: Workspace. Flaps registerQuad: #(SHWorkspace prototypicalToolWindow 'Workspace' 'A workspace is a simple window for editing text. You can later save the contents to a file if you desire.') forFlapNamed: 'Tools'. Flaps replaceToolsFlap.
The class SHWorkspace is a subclass of Workspace so the prototypicalToolWindow implementation comes for free.
The key is to send replaceToolsFlap to the Flaps class otherwise nothing happens. The side effect is the flaps colour schemes are reset (easily fixed) and the Workspace icon is at the bottom of the flap (no idea how to fix but not too bothered).
Thanks, Zulq.