Yesterday you may have seen Darkamons tweet where he shows his New3DS doing a Coldboot (Autoboot) into a bootmanager and from there into rxtools.
— darkamon (@roccocannale) October 7, 2015
Today I’m going to show you how to do this yourself and have Autoboot working on your 3DS. CFW WILL NOT WORK ON 9.3+
1.Start your Ninjhax and turn on Wifi. Start the themehax_installer v.1.2.
It will download and install the payload
2.After the installation just exit Ninjhax. Now shutdown your 3DS and put your SD Card into your PC (or use a card reader)
3.Rename Homebrew Menu boot.3dsx to boot_hb.3dsx. Now copy boot.3dsx and boot.cfg to the root of the SD Card and edit boot.cfg to your needs (Just use notepad).
OR you can use the “more complicated” way and hexedit the menuhax_ropbinpayload.bin file to load the CtrBootManager as menu.3dsx (Just search for boot.3dsx and replace it):
After doing so, you need to change Homebrew Loader in boot.cfg to “boot.3dsx” and save it.
Normal Procedure: RxTools, CakesFW and HBLoader are preconfigured. For RxTools just copy the rxtools folder to the root of the SD Card and download this rxtools.3dsx (If you have problems with this Version please try this version, you only need to copy rxtools.3dsx) and copy it to the root to and change the location in boot.cfg to “/rxtools.3dsx” instead of “/rxTools/sys/code.bin”(Same works for ReiNAND) or copy Cakes.dat to the root for CakesFW. When you are finished put the SD Card back into your 3DS.
4.Start your 3DS while holding the L Button. It should now show the Bootloader Menu where you can boot RxTools, CakesFW, HBLoader or any other CFW. It will autoboot the first option (rxtools) but you can also select what to boot.
To uninstall HomeMenuHax and CtrBootManager just change the Theme to remove HomeMenuHax, delete boot.3dsx, boot.cfg and rename boot_hb.3dsx back to boot.3dsx.
Thanks to Yellow8 for HomeMenuHax, Smealum for HBLoader and cpasjuste for CtrBootManager
Helpful Source: Gbatemp