I assume you refer to the tool "Mounter" which resides in the "Tools" directory of the OS3.9 system partition. If you choose "Mount" in this tool, it will make the partitions available to Workbench. But next time you reboot, you have to repeat this action.
You should run HDToolbox and check the main HDD of your new Amiga. Probably it will tell you that there were some drives added to or removed from the system. If so, choose "save" to make the second drive available. The background is that the first drive has the "this is the last drive" flag set, so the boot process will not search for additional drives. By removing this flag, the second drive will be mounted automagically on the next reboot.
Bye,
Thomas
