Hmmm...

Have you read the install procedures? (I am guessing "no" by your questions)
Summarized and simplified, Linux will ask for permission to install GRUB or LILO into your Master Boot Record (MBR) on your first (boot) drive. Let it. It will not (and really, it can not) modify anything on your Windows NTFS drive. boot.ini is NTLDR's config file, and it will not be used by Linux (unless you go through some manual steps to do it yourself).
Also, you don't need (or want, really) to create filesystems for your Linux install, unless you know what you are doing. Just leave some blank unpartitioned space, and tell it to install in unused space, and it will set up 2 or 3 partitions for you. Minimal effort on your part.