Hope this helps (direct from Hamilton and Palmer who manufacture the alarm for Honda)
have literally done this on a replacement fob today (52 EP3) and lifted this from the leaflet H&P sent through with the fob :-
disarm system - enter car
immediately turn ignition on / off / on / off / on (ignition only not engine running etc)
within 10 secs press raised button on existing fob 3 x (indicators should light up and system LED on dash - now in key learn mode)
press raised button of new handset x 1 (system LED will go out)
press raised button of new handset x 1 (indicators will go out)
done
(obviously this requires the "raised" button to be the right way round in the fobs, thus raised being "lock") - this caused a headache until we realised :asw:
good luck!