I'm assuming your both drives are installed correctly and BIOS sees them without errors.
Go to http://www.masterbooter.com/download/addition … ilities_en.html and download "bootable floppy". Copy this bootable floppy image to an empty floppy disk, boot your PC with that floppy. Run "efdisk". It is a partitioning program, and easy to use, documentation included into the same floppy. Choose your first HDD, create an active primary partition. Do the same for your second HDD, but make it "hidden". Save the configuration and boot with your W98 CD, install Windows 98 as you would normally. When everything related to Windows 98 installation is finished, reboot you PC with the same floppy, and run efdisk again. This time, make your first HDD (in which you just installed Windows 98) hidden, and your second disk as not hidden, save the configuration and reboot with your Windows ME CD. Install Windows ME. After everything you need to do related with ME installation, reboot your PC again with the same floppy. Run mrbooter, and configure your multiboot system according to the documentation. Reboot (without floppy) and you will see a menu screen in which you can choose which windows you want to boot from. You are done.
GA-6VTXE PIII 1.4+512MB
Geforce4 Ti 4200 64MB
Diamond Monster 3D 12MB SLI
SB AWE64 PNP+32MB
120GB IDE Samsung/80GB IDE Seagate/146GB SCSI Compaq/73GB SCSI IBM
Adaptec AHA29160
3com 3C905B-TX
Gotek+CF Reader
MSDOS 6.22+Win 3.11/95 OSR2.1/98SE/ME/2000