Just an update: After I spoke with my supervisor and spilled my frustration (respectfully) she thought about it and then talked to my coworker about my needing to have things ergonomically placed etc. My coworker said she understood. I ended up working with her last night and she was quite nice. I know she will be fine until she has another mood and then we'll go through the same thing but then she will no doubt get over that too.
Thanks all for listening and being a sounding board. I told my sup that I was going to still try and work in the back when my coworker is there just to help things run smoothly and she is good with that. I also told her that I would try to remember to place the keyboard flat when I am done out of courtesy but that I didn't feel like it was my obligation, I'm just trying to play nice. I didn't feel my sup was asking for that but I volunteered since it seemed the thing to do. This way, though, if my coworker gets moody about it, I don't have to feel I have failed if I don't live up to her expectations because there are none.