Is this a desktop machine?
If so, then save yourself a lot
of trouble: install a second disk-drive. Put Windows on one drive; Linux on the other.
To start with, you can use the BIOS Setup-screen to choose either one of these as your "boot-device." In time, you can configure either the Grub or the LILO boot-loaders to load Windows.
The key point is simply this: with this (very cheap) configuration, you have the complete flexibility
that is offered when "Windows can completely ignore Linux, and Linux can completely ignore Windows." You can install Linux, play with it to your heart's content, and do it all
without making the slightest change to your Windows installation.
On my main systems, I actually have three
drives. They're cheap enough, and you can always
find something to do with the space.
Also don't overlook the possibility that many systems can boot from USB 2.0 external disk-drives (or FireWire, if you have it). Those devices (which are downward-compatible with USB 1.1) are very close to just-as-fast as a built-in drive.
Disk drives are, frankly, dirt-cheap now. Nearly every motherboard has two
IDE-interfaces: drop-in cards are also dirt-cheap and may well out-perform the motherboard. Make it easy on yourself and take full advantage of these things!