Unfortunately there is no way to control how WHS distributes the backup.
I have a similar setup to you.
I've got 4 hard drives in my HP EX470 case, and another 3 inside my Mediasonic Pro Box. The beauty of WHS V1 is that you can install any mixture of mismatched drives, I've got a 500gb, two 1tb, two 2tb and two 1.5tb drives. When you turn on folder
duplication WHS will distribute the files however it sees fit, to ensure that the files exist on two separate drives.
WHS V1 was meant to be user friendly, and appliance like, users shouldn't have to think about how the WHS is storing their files. Because WHS is intended to let you mix drive sizes the folder duplication doesn't work the way you've described above.
In my case I'm actually starting to replace my smaller drives with 2tb drives... so I will soon put a new 2tb drive in the last slot in my Mediasonic box, at that point I will remove one of the 1tb drives I've got freeing up a slot in the WHS case..
When that drive starts filling up, I will do the same thing, put a new 2tb drive in the open slot and remove my last remaining 1tb drive.