What's the best way to upgrade from 10.4 to 10.6 - import or upgrade?

I've got an Intel MacPro running 10.4. I bought a 10.6 CD, and want to upgrade. Is it best to 1) install 10.6 onto a clean (empty) new partition and then let Migration Assistant import everything from my 10.4 disk, or 2) ask it to upgrade the existing 10.4 partition to 10.6? My biggest priority is that my system stay as functional as possible (i.e., I don't want it to mess up stuff that worked fine on the 10.4). Is this a risky process - am I better off upgrading a clone (or Time Machine) backup of the 10.4 and booting off that to see how it works, or is this pretty safe and I should just do it? I do have a backup of course. Thanks,
Mike

Be aware that the Snow Leopard installer is more advanced than previous ones & is optimized to upgrade an existing installation.
Among other things, it performs the equivalent of Disk Utility's "Verify Disk" check before it writes anything to the target disk & will not do so if it finds any problems. Thus, you don't need to worry about checking for preexisting directory corruption before running the installer.
The installer also uses the network settings of the existing system on the startup drive (if there is one) to access Apple's database of incompatible apps to get the most current version of it before rebooting from the installer DVD. It may not be able to do this without any existing network settings, & of course if the target drive is empty to begin with you don't get the benefit of that feature, which moves incompatible apps in a existing installation to an "Incompatible Software" folder as part of the upgrade.
The installer will also use what is already installed as a reference for what to install. For instance, if you have existing PPC apps on the target HD, it will install Rosetta automatically. If you have a Quicktime Pro license, it will automatically install Quicktime Player 7 (in the Utilities folder) & reregister your pro license. If you start with an empty disk, neither will be installed by default. The installer will also default to installing 'local & nearby' printer drivers, based on the existing system's printer preferences.
Moreover, unlike earlier OS installers, it never patches any existing OS files to bring them up to the new OS versions, so it is immune to the problems this sometimes caused if the existing versions had any corruption or other damage. Note that it does preserve any preexisting third party system files you have added (unless they are in the incompatible items database) so if they are corrupted or damaged they can still cause problems when the Mac restarts from the newly installed OS. However, since all the actual installation work is done while booted from the DVD, this will not interfere with the installation process itself. For the same reason, the installer is immune to any existing permissions issues, since everything is installed by the superuser running on the DVD's version of the OS.
Basically, while it isn't bulletproof (& for that reason you definitely should have a backup or clone before you use it), the Snow Leopard installer has eliminated the need to perform essentially all the pre-installation steps knowledgeable users often recommend to insure a smooth, trouble-free upgrade to earlier OS versions.
Getting rid of any old 'flotsam and jetsam' is a different matter; however, the installer does remove much of that (or move it to the Incompatible Software folder) & spares users the sometimes tedious task of deciding what to migrate or manually move back into a fresh new system from a backup, which can itself be a source of problems.

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