I'd really recommand some utility software if you're gonna mess with the harddisk.
This allows you to setup partition and cluster sizes from within windows.
The Powerquest stuff (there's a lot, like Partition Magic) has explanations and BACKUP facilities too, so you're safe before applying that final screamer

On the other hand: current harddisks have great performance (bang for the buck) values but imho totally suck in reliability.
That's the price of the price.
To have a separate audio disk will have much more effect than modifying cluster.
The partitioning just keeps files better organized, but doesn't help if (for example) during recording the system tries to access the swap file.
The drive head has to be moved to a different part of the disk - meanwhile the recording gets (hopefully) buffered - then, after the 'system' task the drive moves the head back to the recording track and continues with writing the buffered data.
On two disks this would be a simple channel switch with no mechnics involved.
cheers, Tom