It sounds like you should be using another application like Muse for publishing online.
But you haven't said how you want to publish it. Will this be in EPUB, via Publish Online (new in CC 2015), in PDF, in DPS?
It will be a print format, not digital.
The menu needs to be responsive because this is going to be a customizable manual. I will take the full version, with all of the possible subsections, and remove what is not relevant to the client - saving it as a new version for them. I want each page to reflect that via the side menu without having to redo the menus on every page each time I create a new version for a client.
Which of course, would be easy if I wanted the full toc on each page, but I just want the main sections and the current section's subsections.
How many versions of the manual will be produced? What version of InDesign are you using.
If it's a reasonably small number, you might investigate Conditional Text. You can read about it in InDesign Help.