Ok I went through this crap all day so just some tips. One, browser hax isn't 100% working. When you go to the special website via the QR code it may not work 100% on O3DS. Second, make sure you have gone to themes at least once before you do this because I didn't on my sysnand and when I finally could get themehax rolling via menuhax it had no theme data to exploit. Lastly, definitely use ctrbootmanager. Do a type 1 menuhax install I believe it is. You can then set paths to your launchers and have HBL, RxTools, GW boot, etc.
Homebrew starter kit has junk in the 3ds folder. You really just need Menu_hax folder in it. So just so you are aware, it will have a bunch of stuff you probably don't want, but grab it anyway.