Might need to clear this up a little! Do you have a question about Adobe Captivate specifically? It sounds like it'd be better suited to your purpose; I honestly doubt InDesign will be of much use to you.
I've worked a lot with ID and a bit with DPS. I can't see how you'd use those tools to handle annotation/storing of notes. I'd be more inclined to distribute content to users and advise them to use a 3rd party plugin solution for note taking. As for multiple-choice questions: you can create clickable check boxes in ID's interactive PDF output, but I'm not so sure about doing the same with DPS content. Either way, ID can't handle the logic; you wouldn't be able to program answers, store results, or anything like that.