Going through the programming sequence with the fob or fobs you want to use SHOULD make just that one or ones work.
That is, for example, if you go through the sequence with just ONE of the fobs that would be the only one that will work until you repeat the procedure with both.
"adding" a fob requires BOTH to be present for both to work....
My owner's manual warns that you need all on hand that you want to use B4 starting the procedure for this reason.... Also it mentions that there is a maximum of 4 that can be programmed to work at the same time.
I remember having to do it twice B4 I got it right when I added an extra (only one came with the used car).