You just need to download the latest version of Luma (6.6) and put the arm9loaderhax.bin on the root of you SD card.
Then, paste the "3ds" folder that's inside the "hax" folder and merge, if you already have a "3ds" folder in your 3ds.
At that point, you can try running the homebrew launcher and run luma from there.
You can configure a coldboot after that if you want.
Or even better, you can follow the http://3ds.guide and restore your emunand into your sysnand (this step is almost at the end of the guide)
But how do I get to the homebrew launcher if it tries to boot right into rxtools?