Hi Maurice,
Instead of placing an InDesign file inside of another one, I would recommend embedding the output from another InDesign file using the Web Content interactive widget. The difference is that placing it will export that layout as an image, whereas embedding its output will preserve any interactive features.
If you want to work with separate files, you could export them separately and link to them:
If you're not exporting a responsive layout, then you could use your alternate layouts to help organize your content within one InDesign file.
You can use a navbar with Fixed Position Element applied. If you export your files separately, make sure to use relative links to preserve the paths to the other files. The article above discusses relative links.