Arrange directories, partitions when 2000 also installed

Okay, I have installed XP on my computer and it's a multiple-boot situation. I had problems initially as documented by my other recent posts. Anyway, I now have Windows 2000, XP and Mepis on my computer in separate partitions.

When I am in XP, I see:

My Computer:
Local Disk C: 7.54 GB (Windows 2000), Local Disk D: 224 GB - 142GB used up (this was previously done via Windows 2000 so these are mostly associated with 2000?), Local Disk E: 53 GB (42.8 GB used up), Local Disk F: (Windows XP)

The 'original' Disk D (now called 'E') was being used for Windows 2000 and I used the large NTFS partition for sharing files with Linux. My disk arrangement and spacing got screwed up when I tried to install XP and although it is generally the appropriate setup, I am not sure what to do when installing XP-specific programs or even just to make so that XP has the desired programs (e.g. AVG anti-virus etc.). I thought I needed specific directories for it.

There is another partition on the disk but Windows isn't seeing it which is odd because even Windows 2000 would 'recognize' another (non-NTFS) partition but wouldn't be able to access it. Anyway, that is not the problem. The problem is where to install XP programs and how to configure my disks. I usually create a directory in another partition for downloads and data (so in the event of the OS getting bricked, I don't lose my data).

Is there any good solution? What would you recommend for an efficient configuration?