In the boot process, the BIOS searches for the HD
at the head of its HD boot order. If this HD has a proper
Master Boot Record (MBR), it hands control to that MBR.
The MBR looks for the "active" Primary partition on the
HD, and it hands control to the boot sector of that partition.
That partition is what Microsoft calls the "system" partition.
The "system" partition is the one that contains the loader
and the boot menu, among other things. In WinXP, this
partition contains ntldr, boot.ini, and ntdetect.com. The
files in this partition control the loading the OS, which may
reside in the same partition or in another partition on the
same HD, or on another partition on another HD. The
"system" partition must be a Primary partition, and it must
be marked "active" for the Mater Boot Record (MBR) on
that HD to hand control to it. There may be several
partitions on a HD that are able to function as the "system"
partition, but only the Primary partition that is marked
"active" can be the "system" partition.
Microsoft calls the partition containing the OS the "boot"
partition. The "boot" partition can be a Primary partition
or a Logical Drive in an Extended partition.
There may be many "boot" partitions on a HD.
Explicitly, the "system" partition controls the "booting",
and the "boot" partition contains the operating system.
(Yes, it's intuitively backwards.)
During loading, the menu entries in the boot.ini file
contained in the "system" are used to "point" to the
partition to be used as the "boot" partition, i.e. they
indicate where the OS is to be found.
In the vanilla of vanilla cases (99% of the time), the
"system" and the "boot" partitions are one and the
same, and that partition is the only partition on the
only HD in the system.
Since they usually jumper that HD as Master and put
it on channel 0, it defaults to the head of the BIOS's
HD boot order, causing the BIOS to hand control to its
MBR at boot time, and 99% of PC users then believe
that the "Master HD" must contain the OS to be loaded.
In actual fact, the Slave drive on the primary IDE channel
could just as well control the loading of the OS from the
Master drive on the secondary IDE channel.
*TimDaniels*