1. Boot your mini off its internal drive.
2. Download the free program Carbon Copy Cloner and install it.
3. Plug in and power up your MiniStack (make sure the toggle switch is set to Firwire so it will boot from FW instead of USB2).
4. Launch Applications/Utilities/Disk Utility and format the MiniStack drive and set the number and sizes of partitions as you desire. Quit Disk Utility when done.
5. Launch Carbon Copy Cloner and clone your internal Mini's boot drive to the desired partition on the MiniStack. Make sure you set the "make bootable" option. This will take some time, depending on the size of the contents on your hard drive.
6. When done, launch System Preferences from the blue Apple. Select the Startup Disk pane and choose the bootable partion that you just cloned.
7. Restart your Mac Mini - it should boot from the MiniStack.
8. Once rebooted, launch Disk Utility and format your Mini's internal hard drive.
That's it! This is how I did mine, except that my MiniStack's drive is a single partition (now up to 500 gb) and my internal 100 gig drive has two partitions - a Mac OS install and a Win XP install.