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It shouln't be too difficult, but it depends on your experience. You need to install the second hdd and then install your distribution.
What device name your hard drive will be depends on where you put it. The 'master' drive on the primary controller is /dev/hda and the slave is /dev/hdb. The 'master' on the secondary conroller is /dev/hdc and the slave is /dev/hdd. It wuld help if you know which drive is which.
All but one of the references to linux in your lilo.conf file should point to /dev/hdc (if you placed the new drive as the master on the secondary controller); the 'boot=' should be something like 'boot=/dev/hda' so that lilo can install on the master boot record of your first (hda) hard disk. The only thing that you should change on your primary disk is the MBR (if you want to use lilo - the linux loader). You will also need to add an option to boot your windows partition as well.
A really quickie partition...
/dev/hdb1 /boot 24MB
/dev/hdb2 swap <your RAM size or more>
/dev/hdb3 / <the rest of your disk>
I always put the /boot first on the platters as lilo has some 'issues' with cylinders over 1024. There's a workaround, but this way is easier for me to manage.
A lot of how the installation will go for you depends on your choice of distribution, your hardware setup, and your experience.
For more detailed help you will need to supply some more information.
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