Have you edited your startup sequence to add the command "IDEfix" after the "Setpatch" command? The second channel isn't going to work unless that command is in there, as per the manual:
The installation of the IDE software must be accomplished manually. But,
don't be afraid, this is easier than you probably think. The installation
program mentioned above has already copied all necessary files to your
Harddisk.
To utilize an already formatted IDE drive you just need to add the driver
software called IDEfix in your startup-sequence behind the SetPatch
command. You can do this with any text editor like Ed from your Workbench.
That's it. After restarting your Amiga the harddrive should be
automatically show up.
Just type "ed s:startup-sequence" and insert that idefix command right below Setpatch and save.
Of course, you will need the command "IDEfix" copying over to your c: drawer (but it should be there if you ran the installation).
You need that command, or your second channel where the cdrom drive is connected will simply not work.
Also, instead of using atapi.device, try using scsi.device instead. From reading the idefix docs and cachecdfs, the atapi.device is for A4000 ide ports only, so you should use the scsi.device.
(The scsi.device is built into the ROM chip of your amiga, so no actual file is needed in DEVS:.)
Also, I believe the IDEfix command patches the scsi.device so it can be used with ATAPI cdrom drives. It simply must be in your startup-sequence....