Twice in recent days I have typed in URLS from print and I was more than happy with the way it worked, so this may be a possible route:

Where the text refers to a URL, simply place a superscript reference at the point required and then use the footnote to display the full url.

This technique is used in the recent JISC briefing paper and even more elegantly in the new book by Andy Clarke (Hard boiled web design). – this uses small and grey footnotes as not to distract from the main copy.

When I get your book I will see which technique you opted for 🙂