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!