I did this not so long ago. Went to trade-in my old 3DS for a 3DS XL but wanted to do the system transfer too.
It's worth noting that I did this in the UK and when Tizzy did his he was in the US, so you may find that the shop offers to do it for you.
If you end up doing it yourself, it'll be something along these lines. I was anxious doing it as I didn't want to brick either machine and lose my stuff, but it worked quite easily in the end.
[ul][li]Back up your SD card, just in case.[/li]
[li]You may need to set up some initial system profile on the XL; I can't remember if this is kept after the transfer or not.[/li]
[li]Switch both machines on, go into System Settings, then Other Settings.[/li]
[li]Select System Transfer; let them connect to the internet.[/li]
[li]On the XL, choose Transfer From 3DS; on the 3DS, choose Send From This System.[/li]
[li]Wait while the transfer takes place and spend time watching all the cute little Pikmin running back and forth carrying those bits of card..[/li]
[li]That should be it. The original 3DS will be factory reset and wiped clean and all your stuff should be sitting pretty on the XL. Stick the SD card in and you're good to go - or copy the contents on to a newer, larger SD card. I think you can just fire the SD card into a PC and straight copy/paste the files from your back-up; I don't think you need to put the new SD card in the XL first to get it set up in any way before transferring the files over.[/li]
[li]I had to go back into the eShop and re-download all my VC titles but they were all sitting there waiting.[/li][/ul]
Check this out:
http://www.geek.com/games/how-to-transfer-data-from-your-3ds-to-your-3ds-xl-1510633/
It may not be the exact website I consulted when doing mine but it looks similar, as does the embedded video.
So what happened with me was that I went into the shop, bought the XL for full price and took it home to do the system transfer. Then went back into the shop the next day to "return" the XL for a full refund. They could then give me trade-in credit for the old 3DS, then finally "re-sell" the same XL back to me with the trade-in credit applied.
I had just walked in initially, ended up speaking to the manager and explaining what I wanted to do. It was his suggestion that we followed. Seemed a bit clunky and I had to be able to absorb the extra cost for a couple of days until the refund came through but it all worked in the end.
Good luck, hope it works out for you. Let me know if something goes a bit wobbly; I may not be able to help but there's always trying.
