Thom book 5 is OK. But I found RANT better. Although not a book, it comes with tutorials, demonstrations and exercises which get the message across in a way that sticks, much better that trying to understand a diagram by turning the book at various angles. You can download the demo from
www.oddsoft.co.uk.
The flight planning, enroute, arival, departure, air law, ATC services and wot not that the books don't cover is in the IR theory course material (for JAA).