Ok, so I'm playing New Leaf on the same 3ds as my girlfriend. We each want a town, and I had assumed a digital download + multiple sd cards would allow for this. It appears that an error is thrown up if you swap out SD cards, though, disallowing you to load any save other than the most recent save file.
So. I started poking around the contents of the SD card, and I was able to locate the 2 folders AC creates. They are numbered, rather than human readable names, so I had to go by creation date on the folders to deduce the correct ones.
If you open your SD card on your Mac/PC, you'll notice 2 folders. Ignore private & open the numbered directory. After clicking through another numbered sub-folder, you'll see 3 sub-directories.
dbs
extdata
title
There will be 1 folder you'll need from within extdata & title. Looking inside extdata, click through the solitary numbered directory & you'll see groups of folders that each begin with a series of 0s. The folder I needed was called '00000863'. Not sure if this will be the same for everyone, but go by creation date, to be sure (If your first save was early this morning, the creation date of the folder will match).
Then, move back out to the "title" folder, navigate two levels further & locate the similarly named folder that you found in extdata (here, mine is called '00086300').
Copy both above directories to your machine and insert your 2nd sd card. Pull the same data from that card & you've got backups of both of your towns on your computer. To switch to an older save or different town, just replace the 2 folders on your active sd card (the one you'll be inserting into your 3DS) with the backup folders from your computer. Be sure to back up your latest files before overwriting the live card to avoid losing any data.
If your in a similar situation as me, or if you just want to have multiple towns on one 3DS, this method will work without the need of purchasing a second copy of the game & you only need 1 SD card.
Seems kind of silly but whatever 
