At the template editor, similar to the add-Flash-content button should have a add-Content-Placeholder button. That way templates with content placeholder areas (probably IFRAMEs or DIVs with fixed width/height [or with option to unlock either width or height or both via respective css class setting]) could be added.

Then there should some content editor allowing the user to drag-drop predefined user controls (usually mini apps) onto those content placeholders when editing a page that was made from that template

Also a 2nd step would be to also add a property editor for the custom control properties would be needed for the user to customize the behaviour of more generic controls or of configurable mini-apps