No worries

If you can get one key initialised the other should initialise straight after.
Dont worry about re-doing the lock/unlock and ignition sequence seperately for both keys, just do it once. After you have done the button sequence on the 1st key, wait till the locks bounce then straight away do the same on the 2nd key and it will initialise.
SO;
unlock car
get in shut door
ign on, ign off
press and hold unlock button on 1st key
press lock button 3 times
release both buttons at the same time
locks bounce
----------------
press and hold unlock button on 2nd key
pres lock button 3 times
release both buttons at the same time
locks bounce
If that doesn't work whichever key does not initialise will need to be replaced.