Focus key remote

[ijax1]

My wife has a 2013 Focus Titanium with push button start.
She got a low battery warning for the remote, so I changed the battery,and
now it doesn't work. The remote has a manual key in the fob and I have found
a way to reprogram by using the key in the ignition which is hidden behind a
cover on the steering column. This model can't be programmed that way as you
can't insert the key into the ignition, it has a cradle that the whole fob slides
into and allows the car to start. When this has been removed it is back to
square one, and I have no idea what to do next and can't find any way to make
it work.
Any help would be appreciated.