If you have two drives, pop in the linux CD and select the second drive as the install drive. Put grub in the Master Boot Record of the first drive. Viola!
If you have one drive, I'd do the following:
1) Defrag Windows 98 (you might have to turn off the virtual memory if you have unmovable files)
2) Download
GParted LiveCD and burn as disc image
3) Insert GParted Live CD and reboot.
4) Shrink Windows 98 partition to your desired size (a fully loaded heavy desktop will be like 4GB total, a base Debian install is like 400MB -- no gui).
5) Create swap partition 2x RAM (512MB Max)
6) Create / partition (and if you want a separate /home partition)
7a) reboot into Windows just to make sure you didn't hose anything
7b) reboot into your distro's install CD
8) Go through installation, select partition manually. Choose the new /swap partition for swap, /home for /home, and / for /...
9) Put lilo/grub into Master Boot Record (MBR)
10) finish install and enjoy!
Many people will tell you that you can just use the distro's partition manager to do most of what I did above. I just like to do it separately so that I can reboot into Windows and get a warm fuzzy that I didn't hose anything. Do which ever you're more comfortable with.