for the cd to be bootable you'd obviously need to rip and reburn your copy (or just the win98 directory)
take a look at the msbatch utility on your cd, it should be in \tools\reskit\batch
use this to create your msbatch.inf (it will use your current settings as a base, but I believe you can configure this any way you want)
after you get the file made just include it in the win98 directory and it will automatically be used on installation
To make the cd bootable and to automatically run the setup program you will probably be best off using a floppy and creating the autoexec.bat/config.sys to load the necessary drivers and call the setup program.
I hope this is the answer you were looking for.