It sets up differently. You will have to redo your ini files because everything is now in folders. However, the nice thing about this (very nice) is that you can now use game specific ini files. With 1.61 and earlier, games were only sorted by system and every game had to have the same setup within that system. With 1.62 each game can have different settings within the same system, which makes custom key mapping and such very nice. I dont use this feature much within mame, but for consoles and PC games this comes in extremely handy, especially when using an ipac and it's programmability.
It's pretty easy to setup though. Just make a folder for each system within the config folder and then start mamewah. This will setup ini files for you to edit. At that point it's pretty similiar to 1.61 with slightly different verbage. An experienced person should be able to figure it out.