Thanks for all the help and knowledge. The basement and footings were all dug to the same depth, which I think my earlier post made it sound that it was just the back. It got backfilled the next day after digging with the sand and a little clay mixture from the pasture behind the building site. What I am thinking, is just digging back down to the undisturbed clay and packing it with a packer. We were going to use that fill sand for the floor anyway. The house plan is full basement on the front and both sides, then about half way up with concrete on the back, and the rest framed in with 2x6 walls. The wood framing would have started a bit too low for comfort from the original depth dug.
Again, you dig down so that all footings are at the same level at the top. That means the higher section gets lowered, otherwise, you are going to have to adjust during the poor for the foot difference. As for being too low for the walls, as mentioned before, if the spec's called for a 9 foot wall, you now make it ten feet. Same if it was a eight foot wall, you make it now nine feet. Personally, a higher wall makes for better, when you go to finish the basement area.