I produce several magazines each month. Each magazine wants a digital copy. Right now I am just using the print PDFs to create a booklet and then publishing that on ISSUU. With the new Publish Online Is there an easy way (or any way) to take 16-40 separate pages and use the Publish Online feature to add them to my clients websites?
Make sure you're updated to the latest version of InDesign—InDesign CC 2015.1 (11.1). You should see an option to generate an embeddable iframe code which will allow the page to be embedded in web sites:
Instead of using the print PDF I would suggest to use PDF (interactive) which has smaller size, is always in sRGB, can incorporate TOCs into PDF bookmarks, allows interactivity, etc.
Other part, see Steve's answer.