NetbookInstaller updates your bootloader and extensions etc, every installation disk made with NetbookBootMaker comes with the corresponding version of NetbookInstaller, as long as you're using the latest version of NBBM you won't need to run NBI manually.
However if you installation was made with an older version of NBBM like 0.8.3, you need to download the latest NBI 0.8.4RC1 and run it to patch your installation before updating your OSX to 10.6.3. You run it before doing system update, there's no need to run it afterwards because 0.8.4 automatically take care of that for you. If your installation was done with 0.8.4RC1 then there's absolutely no need to run NBI manually.
Dell Mini 10v, 2GB, 32GB SSD, 56Wh Battery, Snow Leopard 10.6.4, Xcode 3.2.3 and iOS SDK 4.0