You should install lilo on Linux partition (/etc/lilo.conf edition, then lilo).
Then get it to a file
dd if=/dev/hdx of=linuxboot.lnx bs=1 count=512
Now get the file linuxboot.lnx to Windows partition (where you've got boot.ini) and insert to boot.ini
c:\linuxboot.lnx="Linux"
The whole procedure is described in detail in Linux+NT-Loader-HOWTO (in your Linux or at
www.linuxdoc.org).