Generally speaking, the update process I use and recommend is this:
a) visit http://www.apple.com/support/downloads/ and get the correct “combo” updater. There will be several, so pay attention: it’s a big download, so you want the correct one the first time. Set it aside.
b) run disk utility or DiskWarrior or Drive Genius or whatever your favorite drive utility is, and verify that the drive directory structure is OK. If not, fix it.
c) run disk utility and repair permissions
d) clone (preferably) or otherwise backup your drive.
e) some people say to disconnect everything except keyboard, mouse and monitor. (I don’t usually do that, but it won’t hurt if you do.)
f) quit any running programs (except the finder)
g) now run the combo updater.
h) let it do its thing. If it takes longer than you think is should… wait longer. If it auto reboots a couple of times, that’s just fine. Remember “42” and Don’t Panic!
… you know: DiskWarrior, Drive Genius 2; TechTool Pro and so on.
Over the past few days, I’ve had the “joy” of cloning and updating about a dozen drives several times each. Here’s what I’ve learned.
1) don’t have spaces in your volume names. “My_Volume” is OK; “My Volume” is not.
2) if your just-cloned destination drive shows up corrupted when you test it with a drive utility, you have a 99.999% chance that your source drive is corrupted as well.
3) You cannot do more than 3 or 4 (OK: “a few”) drive tests without restarting the disk utility in order to continue successfully.
4) Drive Genius is good, and fast, especially for a quick verify. Knowing I was going to doing all this cloning etc in advance of starting it, I decided to test Drive Genius against the venerable DiskWarrior. What I found was that if DG “verify” said the drive was OK, it was, in fact, OK. If it said it was bad, DW said so too. If DG said it fixed it, DW said it was fixed… and vice-versa. The two programs corroborated each other.
That’s nice because it’s much faster to run Drive Genius Verify than it is to run DiskWarrior.
My confidence in Drive Genius after these repeated tests is high.
As usual, however, YMMV.