Multibooters - System and Boot partitions

When you allow the Windows built-in bootmanager to handle your dual/multi boot arrangement it will require the employing of separate System and Boot partitions. This is because the bootmanager component always remains on the first Windows OS you installed, with subsequent OSes having to be booted through that first OS. The partition with the Windows bootmanager is therefore always the System partition and the OS you are booted into will be the Boot partition. Of course if you only have one Windows then the System and Boot partitions are the same partition.

There is often confusion about which is the actual System partition containing the bootmanager files and which one is the Boot partition that your OS is running from. The easiest way to check is to open the Windows Disk Management utility where you will see the partitions clearly marked as System or Boot. To open Disk Management right click on My Computer (just Computer in Vista) and choose Manage from the popup menu. Once the console opens choose Disk Management from the list of utilities in the left hand pane.

This shows a single install of Vista with the only partition marked as both System and Boot. (Note: In XP's Disk Management utility a partition that is both System and Boot will only be labelled as System).

Adding a second Windows OS will result in separate System and Boot partitions when you are booted into that second OS. It becomes the Boot partition and the original Windows install remains the System partition.

No matter how many OSes or drives you add the System partition stays the same and the running OS becomes the Boot partition. In the example below the booted operating system is on the third partition of the second hard drive.

The System partition always has to be the Active primary partition on the boot hard drive and this can be any one of the 4 primary partitions it is possible to have. The Boot partition can be any primary or logical partition on any connected drive. There is a much fuller explanation of all this on the Understanding the Multiboot Process page.

Independent Windows Installs
If you are not using the Microsoft bootmanager and have installed all your OSes to be independent with each having all their own boot files on their own partition, then they will all be both the System and Boot partition. This will be true for any partition on any hard drive, but the Windows Disk Management utility has problems reporting this correctly for independent installs of Windows that are entirely on logical partitions. Microsoft do not natively provide a way to place an independent install of Windows on a logical partition and so have never given their Disk Management tool the ability to correctly recognise this phenomenon. In XP it can show the logical as just Boot with no System partition allocated, unless your bootmanager can mark logicals as Active. In Vista things can get even more confused with hidden logical partitions being reported as primary partitions.

You say Tomato
Microsoft calls the partition with the boot files the System partition, and the partition with the operating system the Boot partition. Everyone else refers to them exactly the other way round. The boot files on the boot partition. The operating system on the system partition.