I have not done this, but I would-- I saw a post a ways back where someone would put a sticky note on a page where there was errata, so you know to check your errata pages for it, similar to the highlighter idea above.
For 4e I am stricly a player only, so I use CB for characer building (accepting whatever flaws it has, at laest we all use the same rules). The few books I have get out of date, but so be it.
I keep my time and money spent on D&D to a minimum.
I get an heads-up from this forum each time there is an important update, read it and try to remember it. I use the character builder. I might look the rule up from the pdf as I am using a internet connected laptop for initiative tracking while playing.