Personally I make a full copy of the old SD card using "HDD Raw Copy Tool", then I write that backup to the new SD card. Then, because usually you would be upgrading to a bigger card, I use "minitool partition wizard" to resize the second partition on the new SD card (this partition is the one you can see in windows, where you put your files/games, i.e. the big partition). You have to resize the partition because HDD Raw Copy Tool writes a direct copy of your old SD card with whatever sized partitions it had.
I personally find this easier than formatting a new emuNAND and injecting a backup and all that stuff, since I can do it all on my PC. These programs are really easy to use too.