This is normal behavior. The algorithm Drive Extender uses to place files on your server's disks favors the disk which has the least free space, as long as it has enough space for the file. The algorithm also prefers not to place files on the system disk
unless there's no other place for them.
That said, you're correct in your guess that once your server begins to place data on the system disk it will not be able to duplicate that data. Normally, the answer would be to add another disk, but with an Acer unit, I'm not sure what to tell you. I don't
think it has an eSATA port to allow you to connect an additional external drive, and I recommend strongly against the use of USB drives in the storage pool for performance and stability reasons.
I'm not on the WHS team, I just post a lot. :)