You back up, power down, insert the new upgrade/memory card, then power up. The LED will flash red/green for about 10 seconds, then the system will restart. The progrmming will be automatically converted and compatible with the new release. Back it up to the new card, and leave the new card in place. Throw the old card away, or save it for reprogramming if you are an Avaya Business Partner.
On a 1.0, you have to replace the whole ACS! Just got done with one where the salesman sold an R5 upgrade card and a PC Card VoiceMail, without checking on the release first. Found out it was an R1, couldn't upgrade, customer had to buy a new R5 ACS to get the V.M.