Hello. My name is***** can help you with your question.
So, I think your question is that if you have need to cards in and you have filled the first card, what happens? The functionality of the 2nd card slot can be configured for different purposes. And you select those purposes. Here are the options and this is from the Nikon guide
Slot 2 top
The Nikon D3 has two full-function CF card slots. They just work. This menu selects what the second slot does.
Poke a card in either slot and it just goes. The top display and the bottom display always tell you which card is doing what; and on playback which card is being read is shown on-screen. Brilliant!
Poke a card in each, and if the first card fails or gets full, the D3 just writes to the second card.
If you bend the pins in one card slot, just use the other.
By default, the second card is used only when the first card fills up ("overflow").
If the first slot is empty or the card dies or has problems, the D3 simply writes to the second card.
In this position, you never need to tell the D3 to which card to write. If you're using only one card, use either slot.
I use this position. (MENU > Shooting > Slot 2 > Backup).
As you shoot, the D3 writes to both cards.
This completely revolutionizes my workflow. Security protocol prohibits me from formatting a card unless the files exist in at least two other physical locations. In the old days, even when I copied to my hard drive, I would not format my card until that hard drive was backed up, and that backup was taken to a second physical location.
Now that I have copies of all the files on the second card in-camera, as soon as the files are on my hard drive, I may format the first card with reckless abandon. Whoo hoo!
The D3's brilliance starts as you delete images and format cards. When you delete, you're usually only deleting from card 1. When you format with the two red buttonsyou're only formatting card 1 (unless you go out of your way otherwise). As you shoot and screw up, card two is quietly recording everything and not deleting anything. It's all there on card two.
The only design flaw is that when card two eventually fills up, you're screwed because even if there's space on card one, the D3 stops shooting! Regardless of the size of card two, since the D3 is copying everything as shot, but not removing it from card two as you delete and format, card two will fill up right when you don't want it to. Be sure to format card two every so often (use the menus, or hold one of the two red FORMAT buttons and flick the rear control dial when "For" is blinking to select card two) so you have enough room.
You may want to buy a big, cheap card for slot two, but it will still fill up.
The "Slot 2" setting is in a menu which is saved and recalled as you call up Shooting Banks. If you think you're being safe setting the second card as backup, but then select a different setting bank, you no longer will be using the second card as backup!
In other words, I use one Shooting Bank in my studio, and another outdoors. When I move from one location to the other, I instinctively change to the appropriate, named Shooting and Custom Settings bank memories. If I set Slot 2 set for backup, it won't be set in the other bank unless I set it that way again!
Format all you want using the red buttons and only card one is formatted. Card two is left alone, unless you have card one pulled because it's in your card reader! If you have card one removed and hit the red Format buttons, the D3 dutifully will format card two.
Pay attention! The D3 very clearly shows on the top LCD which card is being formatted when you hold down the red buttons, but I know if I did this often in the field I'd screw up.
If you don't plan to use the second slot, at least plug it with an old, low-capacity card you were going to throw away.
This way, if you forget to insert your regular card or it fails, you'll still be shooting on something.
Let me know if after you've read that you still have questions. I'll be happy to help until your question has been fully answered.