So the big question is on many gamer's minds is what is the best way to transfer from an old 3DS to the New 3DS with the MicroSD card proving to be something that might cause confusion. The key point I got from this:
1: Copy your data from your old SD Card to your PC before buying the New 3DS and a new MicroSD card,
2: During the transfer process, chose option 2 i and only transfer the limited amount of data between systems (not the games, just I.D's and licences)
3: Then after the system transfer is completed, copy the contents of your backup file from your PC to your new MicroSD card and insert into the already fully transferred New 3DS.
After doing this, everything on the New 3DS should look exactly as it did on your old 3DS. Sounds simple enough right?