never tried CFW, but if it's the same with GW, for SD card with smaller size personally I'd choose to use
emuNAND tool
on the old SD card
1. create emuNAND.bin using emuNAND tool. keep it somewhere safe
2. backup all contents of your old SD card somewhere, simply using Windows Explorer or any file browser
on the new SD card
1. create emuNAND partition using 3DS (can also use GW create emunand feature)
2. inject NAND dump to new SD card using emuNAND tool
3. copy all backed up files to new SD card. if you are limited in space, you can choose not to copy unnecessary files (photos, etc)