I'm not entirely sure I understand but here's what I think:
I believe you can only install GoBack on the same drive as your operating system. I assume you are not installing an operating system on your slave drive: GoBack won't work on multiboot systems.
If you do fresh install on your WIN98se drive I believe you will be given the option for GoBack to also monitor your 2nd hard drive, though the usefulness of this is questionable.
If you want GoBack to monitor both drives I would uninstall it, reinstall and during the installation choose the option to monitor both drives.