In an ideal world, paper might not be necessary. In a next to ideal world, one would have enough time to write a hypertext version of a document and also to write a completely separate paper version. However, the real world, you will probably want to generate any printed documents and online documents from the same file.
Suppose the HTML files will be the master, and you will generate the printable from this, by making one long document, and possibly printing it via translation into TeX, or some word processor format, for example. You might not initially, but you might want to one day.
Try to avoid references in the text to online aspects. "See the section on device independence " is better than "For more on device independence, click here .". In fact we are talking about a form of device independence .
Unfortunately, the recommended practices of signing each document and giving navigational links tend to mess up the printable copy, though one can of course develop ways of stripping them out if they follow a common format.
For example, the most common comment about this document was that it is difficult to print. I therefore made a single page version of the whole thing with a few scripts, and put a pointer to it from the cover page. But then people still ask, not having read the cover page. (The scripts were just bits of "sed", which I am not supporting. I have put rules in at the top and bottom of each page and the scripts use these to chop off bits which are not needed in the printed copy.)