The first digital publishing tool I worked with is Mag+ plugin for Adobe InDesign. What I really like in Mag+ is a layer system. In Adobe DPS I also use layers, usually I create a layer for every interactive element.
This is example of a pop-up page layers. I have 3 layers: Background (images + text), Buttons and MSO (Multi State Object). This is Mag+ standard layer panel. This is my favourite feature, I can make a “Device portrait / landscape” layer visible and a tablet image appears. Very useful, if you want to see how the page looks on device without previewing.