it will work perfectly for win98, and i am not 100% sure about IExplore 6, but i tried it with 5.5 and no problems.
It's odd that you can't get true dos mode from win98.
If i were you i'd go to the start menu, select shut down, and you should get 4 options, 'shut down', 'restart', 'sleep' and 'restart in msdos mode'
Of course you choose 'restart in msdos mode' and it just boots up to a command prompt, which should look like this:
C:/WINDOWS>
This means you are in the windows folder/directory on the C: drive, that's the folder where windows is installed (unless you put it somewhere else, but that's highly unlikely).
to get to this prompt, you might want to try that F8 thing, or i have heard that sometimes it's some other F* key that you need to press.
That's all i know!