I personally don't have windows on my machines, but when you install VL your windows will be detected and a proper lilo is setup. But please be aware that VL5.9 is NOT ready. It's just a VERY basic setup. It's mainly for packagers/developers to have a base to work off of, and advanced users to play around with.
You really should be using VL5.8 Standard/SOHO
But if you would like to try VL5.9x, be warned, it has quite a while to go before it's user friendly. It is usable, but plenty of things do not work at this time. And.... since it's so young, the install is painfully slow. So run setup, and go mow the lawn or something.