You run the fdisk program from the C:\WINDOWS\COMMAND folder. Choose the option for selecting the disk(where you should select the disk that's newly added). After that you need to create an extended partition and logical drive.
That's explained in https://www.youtube.com/watch?v=satl8PNW_DI . Go to 4:50 for the extended/logical partition on the second drive(don't forget to change the selected drive to the added hard drive(#2 probably) first!).
Then, after rebooting(reboot windows if done from within windows 9x. If from MS-DOS, Ctrl-Alt-Del will do the same). If done correctly, the BIOS should start booting Windows again(don't forget to remove any floppy drives if it's set as a bootable drive in the BIOS settings).
Then in Windows 98, you can simply select the drive and if you try to open it it'll as to format it. Confirm and simply format it using the tool(if it doesn't appear, right click the drive and click on the Format option).
Enter the filesystem information etc. and click the button at the bottom to start formatting the drive.