One thing that you rarely learn before starting a faculty job is how much work goes into managing a research group. During my pre-tenure days, this meant squeezing the most productivity out of my students and making sure they were hitting on all cylinders. Now that I have tenure, my role is more like a bodhisattva -- simply to make sure that my students (and postdocs and research staff) are successful in whatever they do. Of course, productivity and success have a high degree of overlap, but they are not exactly the same thing.
There are many subtle things that one needs to know to make sure that a research group is functioning properly. A lot of it has to do with making sure that the personalities mesh well. For a while, I tried to get all of my students to work together on One Big Project. We would have these big group meetings and write design docs but over time it became clear to me that it just wasn't working. It finally dawned on me that a couple of the students in my group (including one who had developed most of the core code that I wanted everyone else to rely on) were not that interested in working with other people -- they were far better off doing their own thing. I've also had students who really work fantastically in a team setting, sometimes to a fault. Those students are really good at doing service work and helping others, when they really should be more selfish and pushing their own agenda first. In general it's good to have a mix of personalities with different strengths in the group. If everyone is gunning to be head honcho, it isn't going to work.
Of course, most junior faculty go into the job with zero management training or skills. One's experience in grad school no doubt has a big influence on their approach to running a research group. My advisor was David Culler, who is known to be extremely hands-off with his students (though he can do this amazing Jedi mind trick -- to get his students to do his bidding -- that I have never quite mastered). I took after David, though I find that I am much happier hacking alongside the students, rather than only discussing things at the whiteboard. I also see lots of junior faculty who live in the lab with their students and have their hands all over their code, so there are many different paths to enlightenment.
All along I wished I had more management experience or training. Early on, I was given a copy of Robert Boice's Advice for New Faculty Members, and frankly found it to be fairly useless. It is unnecessarily cryptic: the very first section is entitled "Rationale for a Nihil Nimus (Moderate) Approach to Teaching" -- I am still not sure what the hell that means, but it certainly wasn't any help for someone starting up a big research lab.
It turns out that MIT Professional Education runs a short course on Leadership Skills for Engineering and Science Faculty. (I signed up for this a few years ago but they canceled the course due to low enrollment! I certainly hope to take it one day.) Another useful resource is the Harvard Business Review Paperback Series, which is a collection of (very short and readable) books on management topics, some of which are germane to science faculty running a lab. For example, the book on motivating people gets into the various ways of getting your "employees" (a.k.a. students) to be productive, and talks all about the pros and cons of the carrot versus the stick. Synopsis: If you can get inside the head of an unmotivated student and figure out what they want, you can motivate them to do anything. This must be the key behind Culler's Jedi mind trick.