Okay so you want to move your backup aps to a new sd card? Correct?
I think... Just put the card in the phone, mount, and move over. They should be in folders all ready, I don't think the card has a special folder, at least mine doesn't. I have various folders for items, but no specific main folder.
When I mount it on my work computer it shows up as the 'G: Removable" drive (unless I have something plugged into the other USB drive.
So everything is under the G drive.
If you have folders on the new SD card all ready, it may overwrite them, if not you can delete the empty ones.
This is something that I have been wondering as well. I data wipe and flash roms every now and then and have been wondering if all my apps on the sd card would continue to occupy space on their own partition.