The basics are:

1) Back up your data off the machine if you have not so yet.
2) At the A:> prompt type in format C:/S, accept the format
3) Put the Win98 cd in and at the A:> prompt switch to whatever drive the bootdisk has assigned to the CDrom drive, likely E:
4) At the E:> prompt type in cd win98. At the E:\win98 prompt type in setup, and you are off to the races.
5) After Windows installs it's up to you to supply motherboard/modem/video/sound/etc... drivers for your various devices.