Why? Sky3DS only supports 3DS ROM's and switching games is a major PITA. Not to mention, I have a Mac and copying games to the Sky3DS is also a PITA since I have to use VMWare.
Press the blue button till you find the game you want to convert
Hold L while starting the game and wait for the top screen to flash green twice then hit A to continue booting the game. Luigi's Mansion never loaded for me, but the save got created just fine. I just powered off my console when it got stuck at the startup animation.
Shut down the N3DS and boot into Gateway Mode
Mount the ROM and create a new savegame if you don't already have one
Close the game and power down the N3DS
Eject the SD Card and put it in your PC
Rename the save from whatever title ID it is to 000400000FF40A00.sav
Boot back into Gateway Mode and mount your ROM
Launch SaveDataFiler
Highlight CTR-Card and press Y then A to export the "dummy" save game we created
Close SaveDataFiler and power down the N3DS
Eject the SD Card and put it in your PC
Copy save_%titleid%/profile1.sav to filer/UserSaveData/DATE/TITLE/profile1.sav
Boot back into Gateway Mode and mount your ROM
Launch SaveDataFiler
Switch over to SD and highlight the title ID
Press L + A and then A to import the save to CTR Card
Close SaveDataFiler and power down the N3DS
Eject the SD Card and put it in your PC
Copy 000400000FF40A00.sav to titleID.sav
Boot back into Gateway Mode and mount your ROM
Profit!
I hope this saves someone the time and effort it took me to make this work. Now I can finally get back to finishing this game!
P.S. if you already know the folder structure for SaveDataFiler you can skip the "dummy" save game creation and copy profile1.sav directly to the proper location and create 000400000FF40A00.sav from an existing save. This will save you a bunch of time.