Systems that cant emulate EFI or early EFI emulated systems are subject to crashes after a update. Even if the update is OSx86 compatible it can still be unstable due to the hardware that is in play.

To make things simple I create a three partition system with a single 160GB hard drive (Plenty for my needs).

System 8GB - Main OS partition
Main 52GB - Holds Users directory, custom extensions and backup use
Applications 100GB - To store all of my applications

Installed the system like usual onto the System partition. After the install was complete I copied the Applications to the Applications directory and the Users directory to the Main partition. I rebooted and used the install CD once again and used Terminal and deleted the Applications directory in the System partition and issued this command ln -s /Volumes/Applications/Applications Applications This creates a shortcut in the System partition. I did the same thing with the Users directory and Main partition.

For my custom extensions I created a bash script that copies and sets the permissions.

I also created a disk dump of the System partition and burned it to a double layer DVD so if things mess up I can use a Linux Live CD and restore the partition and be back to normal. But in all if the system crashes I can just reinstall but if I update to say 10.5.6 that works flawlessly I can use a updated disk dump.

Also this method can be used with multiple drives.