Re: W98se Drivers.
From your description, the CD sounds like those distributed with PC Chips motherboards circa 2000 to 2001. The AutoInstallation feature relates to install Windows drivers.
If you format your hard disk, run the standard Windows 98 install from CD (using either a bootable CD or a bootable floppy disk with CD drivers in Config.sys and Autoexec.bat) you can then insert the System Board CD and, if it autoruns, the install dialogue box will come up.
From there the Setup.exe will detect your version of Windows and what components the Windows installation has got right (that is the Auto part of AutoInstall) and configure itself to install the rest. This may take several re-boots.
Because Windows may not have installed drivers for all devices after the second re-boot during Windows install you will be advised of new hardware found for which Windows does not have a driver. Just Cancell these. Likewise after the AutoInstall process, it will bring up a dedicated dialogue to install each device.
Of course, it could be the CD you have is not for your motherboard. If you look at the contents of the CD using Windows Explorer you will find a number of text files which, in varying degrees, will list the motherboard models it caters for.
If you do not know which motherboard you have, look carefully at the markings on the motherboard, the model is usually screenprinted somewhere. If you have a PC Chips motherboard the model will start with an M, probably M7.