Finally I got my wd 40GB HD from buy.com( ata100, 7200rpm for $133 if you care ). I did install Windows 98 in this HD and I can boot all my OSs of Windows 98, W2k and Linux, but I have to switch the boot from BIOS.
Following is the process:
Pre. Setup:
wd 18GB HD on IDE1, Master
Hitachi DVD-ROM on IDE2, Master
New Setup:
wd 18GB HD on IDE1, Master, I cannot put this one on another IDE channel, because Linux will complain.
wd 40GB HD on IDE2, Master,
Hitachi DVD-ROM on IDE2, Slave
During setup, unplug IDE1 cable, so I made sure the installation will not overwrite my 18GB HD.
Go to BIOS setup( I have ABIT BX2.0 ), change boot sequence to "D:..."; I think that "D:" is the second harddrive not the second logic drive. Then I installed Windows 98 as usual.
All in all, I have to go to BIOS to switch boot sequence to boot either from W2k/Linux or Windows 98.
I did try to setup Linux lilo table(/dev/hdc for my wd 40GB drive and /dev/hdc1 for Windows 98 c

, but still cannot boot it. Anyway, I am pretty happy with my current configuration.