Ok, a few things here. First off, if the SATA drive contains your primary OS, that means you set it to SATA port 0. Which is just fine. What you don't realize is that ( unless I'm mistaken ) Sata port 0 takes precedence over IDE 1 master.
I assume you've used microsoft's bootloader toswitch between Windows installations, but traditionally microsoft says its too complicated to install windows on another than the primary drive. Hats off to you, you did a good job till now, its actually going exactly as it should.
When you came to install win 2000, it saw the drive as D:, because windows XP designated it as D: Win2000 must have detected the windows XP, and knows better than to fiddle with the drive letters like this. XP needs the C:, so 2000 used D:
As for changing the programs drive, that one is easy.
go into the registry, please. It's important to remember that the registry is quite possibly the most sensitive area of your Windows. Never delete any keys unless you've exported them first. Never change anything unless you're asked to by one of us. We have experience with the registry, you may not have any, or very little.
start menu/run/ regedit
Now, in the right pane, locate the following key
This setting is usually associated with C:\Program Files
Change it to D:\, like so
That's what you should see in the window now.
If you want to use D:\Program Files, type it in. Just copy and paste the directory you wish to have it use.
All this is done from within your windows 2000 by the way. After it's done, reboot, and test an installation. It should be using D:\ ( or D:\Program Files ) now.