I'd like to let you all know there's a little known 3rd option to flashing your oothax save.
Minimum Hardware Needed:
DSlite/phat + DS flashcard.
1. Download DSsavemanager
http://3dbrew.org/wiki/DSaveManager
2. Download the save files here
https://github.com/yellows8/oot3dha...t3dhax_rawsaveimages_haxpayloads_11-10-15.zip
3. Find your 3ds's save in the raw 'saveimages' folder (refer to the oot3dhax repo readme). If you don't know what card remaster type you have, just grab both.
4. Place the 2 raw .sav files and DSM.nds in your DS flash microSD
root.
5. This is the tricky part. You will either need to saw off the nub of the corner of your zelda cart or open it, take out the board, and place it in a ds card shell.
6. Now boot up DSM.nds and select "Restore save(FAT)" Find your save and select it.
7. Replace the DS flashcard with OOT and Press A to write the save. Done! Enjoy your OOT3Dhax. (if the 1st save didn't work, try the second)
I have tested this method and it works.