Ok here is the deal, I currently have a normal 3ds (let's call this 3ds 1) and I have a Fire Emblem 3ds XL which I haven't opened yet (3ds 2).
I also have a new 16gb SD card that I want to end up with all of my data on at the end of this.
What are the steps that I should take where I will end up with my Fire Emblem 3ds XL with the 16gb SD card as well as all of my 3ds 1 info as well as the pre loaded software Fire Emblem originally from 3ds 2?
First, move all of the datas from your old SD Card to the 16GB one. Leave that on your 3DS #1.
Second, initiate System Transfer, with 3DS #1 being the source system, and 3DS #2 as the target system. Do not swap the SD Cards until you're nearly finished and the systems prompt you to swap SD Cards.
All of the datas from your 3DS #1 will be merged with the apps from 3DS #2. Your copy of Fire Emblem: Awakening would be erased, but you can redownload it without any extra charge, even if you transferred everything from your 3DS #1.
Mind if I pop in for a moment as I have a similar issue. Since I'm getting the AC 3DS XL bundle, is it possible to do the system transfer and merge the data on the SD card without it erasing New Leaf and me having to re-download it???
I don't think that's even possible. You'd still need to take the SD card out from 3DS #1 and then put it in 3DS #2 after the transfer. That's because the target system won't recognize the data from the SD card that was originally included on 3DS #2.
This page explains how to transfer software and things from one 3DS to another here.
The ACNL from that bundle is tied to 3DS #2. If you were to carry this data to your current SD card from 3DS #1, the game won't be recognized by that 3DS, since you haven't downloaded the game in first place. In short, it's practically useless to do this trick. You're stuck to redownload ACNL for around 30 minutes (assuming you have a reliable 512+ kbs Internet Connection) after the transfer.
