Installing windows 98 on an old computer?

I'm trying to put together an old computer, an so far its gone really well till this one road block. I've used a bootdisk bootwindows 98 in the command prompt and have followed as best I can the directions on using it. At this point my problem seems to be getting the computer to recognize the cd drive as its own master drive, so far all its done is be a slave to the master harddrive on bootup, and from what I read on some instructions I need to copy files for the cd drive to auto run an operating system disk. I'll probably figure it out eventually but help will be greatly appreciated and save me some time