I suggest the following layout:
Drive 1 - NTFS:
1: Windows install
2: Storage Partition
Drive 2 - GUID/HFS+J non-case sensitive (prepare using Apple Disk Utility)
1: OSX partition - first install an easy to install distro like iPC or something.
2: storage partition
3: an 8GB partition that holds the contents of a 10.5.6 Leopard DVD so that you can easily install retail to the first partition.
The idea here is to make an image of your retail Leopard DVD and then use Disk Utility to 'restore' it to the 8GB partition, instead of burning it to a DVD. It will become clear to you what I'm talking about once you open the DVD image with Disk Utility. You'll want to do this because it's much easier, not to mention faster, to install from a partition on your HDD than it is to install from DVD.
Once you've got Chameleon set up on the EFI partition with your required patches and modifications, you then use it to boot straight into the retail 10.5.6 installer on the 3rd partition.
You might want to use the bigger drive for Windows and the NTFS storage partition if that's where you spend most of your time. If you have a huge media collection you can still access all of it from within OSX, you just can't write to it. There are NTFS drivers for OSX that work (Paragon NTFS, and MacFuse with NTFS-3G) but personally I prefer to keep it read only.
Come Snow Leopard, there may be a fully functional HFS+ driver for Windows. Until then you can use Transmac or MacDrive under Windows for R/W access to your HFS+ partitions. It will be no surprise that I don't trust those either, but they can be useful.
When formatting as GUID the invisible EFI partition gets created automatically like on a real Mac.
The problem with this is you'd need a third hard drive to juggle all your data around when making the changes. Or, unless you have a Blu-Ray burner, a hell of a lot of blank DVD8 discs and a dependable DVD burner.