Hints for making a bootable partition on extra hard disk

Hi all - I hope that my query is unique enough to merit being ranked as a question.
I have a G4 that I bought from a friend. Its original HD was a SCSI, and I just had a larger ATA drive installed, while keeping the SCSI. The ATA is now my main startup drive. I have it divided into three partitions - one is my main startup & system & applications, the other for storage, and the third for OS 9.2. I have just upgraded to MacOS 10.4, with the latest updates.
I have backed up all the data on the SCSI and deleted all the files on it. The SCSI HD has three partitions that I want to convert into two ( or maybe just one, depending on your advice ).
I would like to have one of the SCSI partitions be bootable with 10.4, as an emergency/backup startup disk. The other partition I want for media data storage - graphics and music, maybe video.
My questions:
1. What file system should I use? The ATA drive is using "Journaled HFS+", what would determine if I should use another type for the SCSI partitions?
2. Do I need two partitions? In a quick reading of the discussions, it seems that some folks think that, unless you're running a different operating system in each partition, there is little other reason for partitioning a hard drive.
3. Do I use my 10.4 installer DVD to make the bootable SCSI partition? Or are there ways that are more apt for what I want to do?
Thanks for reading this far!
G4 AGP Graphics M5183   Mac OS X (10.4.8)  

You might need to give more info on the two HD's.
size?
Also, how old is the SCSI? Drives tend to start
acting crazy at 5 or 6 years old.
The SCSI drive is the original, so it's probably close to 7 years old. It's an 18GB Seagate ST318203LW. The new ATA is a 160GB Hitachi HDT722516DLAT80 (usable storage is actually 128GB).
You probably had to partition the new ATA drive
because your G4 doesn't recognize drives sizes larger
than 128gb.
The ATA is partitioned the way it is because I had the SCSI partitioned in a similar manner - one 10.3 partition, one storage partition, and one 9.2 partition. I had the MAc service shop do a clone from the SCSI to the ATA, with the only difference being that the partitions are bigger. There are no plans to repartition the ATA.
I want to repartition the SCSI and install a backup startup capability, while alos using the SCSI for media data storage - graphics and music, maybe video. Since the SCSI drive is old, I'll make sure they're noncritical files.

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