Sorry for the late reply on your question Dave.
In regards to your first question, yes, if you only delete the photos from one card then they will remain on the second card.
In regards to your second question, the second card only gets reformatted if you reformat it as well. Otherwise it is left alone, regardless of what you do to the first card.
In regards to the third question, nothing happens to the second card at all unless you actually do something to it to delete pictures from it and/or format it.
A couple more points worth noting:
1 - You are doing the right thing by reformatting it each time. Cards are prone to write errors when used in digital cameras if you don't format each time and just delete pictures from the card. I have had that experience myself.
2 - One of the reasons the second (backup card) does not delete pictures automatically when you delete them from the first card is because if you accidentally delete a picture from the main card then you still always have a backup available until you actually delete it from or format the second card.
3 - At the moment I am shooting with a 16GB CF card and a bunch of 2GB and 4GB SD cards as backup. When I put the 16GB CF card into the camera with a 4GB SD card it tells me I only have 200+ pictures left I can shoot in RAW, even though the 16GB CF card is capable of capturing close to 1,000 RAW pictures.
Basically, the camera, when you have it in backup flash card mode saving to two cards, only allows you to shoot as many pictures on your main card as you have backup space available for on the second card. So this way when the backup card is full I am able to know that and change the backup card to a fresh empty one at that point. Then I am able to keep shooting on the main card again until the backup card gets full again. So my backups get spanned over a number of backup cards, but all of my pictures are saved on one main CF card. Eventually I will get a 16GB SD card to match the 16GB CF card, but for the moment this system works. They just came out with a 16GB SD card by the way in case you would like to see:
http://www.newegg.com/Product/Product.aspx?Item=N82E16820220254&Tpk=16gb%2bsdhcI hope that helps.