If you are trying to inter mingle the SMIL tags with the InDesign export you are going to have a hard time. I got a proof of concept working where you put the SMIL at the end of InDesigns export, a sort of overlay. Even built a plugin to get the SMIL ( geometry ) positions working.
The link to the sample ePub is broken, I will try and find the file and post a link so you can rip it apart.
The project died, lack of interest :-(
That's too bad the project dried up. There is an app for the Mac called Circular Flo that you may have heard of that is supposed to generate the necessary code and then recompile it all back into an ePUB file. I'm on a Windows machine so it does me no good. That said, I'm doing this manually, which is fine because it's good to know what's going on under the hood on these documents.
I've read this post by Alberto Pettarin and also read Chptr 6 Media Overlays of Epub 3 Best Practices, which did shed some light on the process, but I'm still striking out with getting it to work. I know someone who managed to do this with InDesign, but she's very hard to get hold of, that's why I posted here.
I'd like to have a look at the sample ePUB. Def let me know if you find it.
I will dig the sample out or create a new one.
Here is a sample of what our ( now dead ) plugin did.
Rip it open, there might be some useful snippets in there for you. Quite interest to know how / if it works on windows.
CircularFlo is excellent and well supported. Problem for me is that it is Mac only.
I don't know why software companies still write apps just for the mac in this day and age. There's a whole other market of Windows users who design and develop.