Install AppleJack on the other boot drives and boot from them into single user mode. Other than that, there is no way to use AppleJack on them. It's unfortunate, but due to the way the underlying utilities work, AppleJack can only work with the boot drive that's currently active.

You can however, do basic troubleshooting on one of the other drives via Disk Utility. Check your other mounted drives for errors, and repair the permissions. That, at least, is possible.