In reply to:

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Or is it even sufficient to just make sure the music
partition exists, having the same number (5?) as the one on
the primary hd (ie. /dev/hdb5 if the music partition on the
first HD id /dev/hda5)? If the same partitions have to exist
(no matter if they need to be the same size), could 3rd
party software use its aequivalent of the scratch partition?

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No need to replicate the partitions, I only have one partition
on my second disk, the music partition, /dev/hdc4, see below.
/dev/hdc is for a MkI, IIRC MkII uses /dev/hdb.

About what might be touched in the partition table - no
idea, but I think I recall empeg saying that the table on
the second disk would never be touched - someone please
correct me if I'm wrong here!

So as long as you have hd[bc]4 for the music you should be free to use other partitions as you wish...

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empeg:/empeg/bin# fdisk /dev/hdc

The number of cylinders for this disk is set to 35152.
There is nothing wrong with that, but this is larger than 1024,
and could in certain setups cause problems with:
1) software that runs at boot time (e.g., LILO)
2) booting and partitioning software from other OSs
(e.g., DOS FDISK, OS/2 FDISK)

Command (m for help): p

Disk /dev/hdc: 16 heads, 63 sectors, 35152 cylinders
Units = cylinders of 1008 * 512 bytes

Device Boot Start End Blocks Id System
/dev/hdc4 1 35152 17716576+ 83 Linux

Command (m for help): q

empeg:/empeg/bin#