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The manual is old and some things have changed or been added, though the overall approach of the program has been stable. The built-in documentation (Help menu) may be somewhat more up-to-date, but the manual has never done much more than describe the basic features of the program, as wilsonng points out. It doesn't discuss how you might use the tools provided except in the most basic fashion, but if you read the forum, you'll discover that there are many ways you can use the tools, some of them not all that obvious at first glance! The AsianEfficiency pages, Kourosh Dini's excellent Using OmniFocus ebook, MacSparky's videos, etc. all attempt to fill a bit of the vacuum between understanding how to manipulate the program and using it effectively. The manual tells you how to operate the keys and pedals on the piano; building on that knowledge to become a skilled musician takes some time, practice, quite a few wrong notes, and imagination (and/or a willingness to investigate what others have done before you).

You should definitely watch the videos on the product page: http://www.omnigroup.com/products/omnifocus/videos/
(MacSparky's videos are linked from that page and deserve your attention, though you may be able to skip over some of the material if you don't use the iPad, for example).