You should be able to do both together, one after the other using the same coding instructions. Only a max of 2 fobs can be coded for the YRV Door opening mechanism.

From memory you have only a few seconds between coding each fob to do it though in one continuous sequence. If you are doing this by trying to do each 1 using the remove and replace then it will only code the last one you did it with.
I have 2 fobs coded to my YRV using the continued sequence method.

I take it you are doing the remove the negative terminal for 15 seconds replace negative terminal and pressing the buttons on the key fobs method?