I agree with bookworm; you can do just that. My only caveat, and this is a bit hazy. I believe I skipped that bottom 1GB partition and went with only the partitions containing programs in each of the remaining 500GB (or less) partitions. I had 1.5TB EHD's so one of my 500GB partitions was also a bit less.Does it matter which folder I put the copied files in? Do I follow the same pattern and fill the folders from the bottom up? I anticipate filling the bottom folder from the donor drive to the bottom folder on the target drive, and work my way up from there.
Why does Dish partition EHD's like this? I don't know, but it benefitted me greatly when one of my WD Greendrives semi-crapped out. Only one of the 500GB partitions became unreadable, so I was able to copy the remaining programs onto a new drive that WD sent me and I was happy. As near as I can remember, it was the uppermost partition and there was nothing on it. So I lost nothing (other than the bad drive).