the instructions an the GW website aren't exactly noob friendly, here is a improved version
1) Copy the Gateway 3DS 3.2.1 ULTRA Launcher.dat to your New 3DS microSD card
2) Copy mset_<region>.cia and bluecardfix.cia to your New 3DS microSD card (where <region> is your console region)
3) Copy “DevMenu.3ds” to your Gateway 3DS microSD card.
4) Boot into the Gateway menu with your preferred entrypoint (Zelda or Cubic Ninja)
5) Select the new “NVRAM INSTALL” option from the menu, proceed with installation.
6) Once installed, Hold B and choose Gateway mode, it will warn you that your are booting into sysnand, press X to continue.
7) launch DevMenu.3ds(do not use bigbluemenu.3ds, this will not work with BBM) from the multirom menu (press SELECT)
8) Start DevMenu and import mset_<region>.cia and bluecardfix.cia from your SD card.
9) Reboot console and verify you can now boot into Gateway mode with the classic System Settings DS Profile method. (Settings -> Profile -> Nintendo DS profile)
10) Enjoy! No more cartridge swapping required to use Gateway 3DS on New 3DS!
this will allow you to use the new gatewayinstaller.nds file on the blue card, so you will technically never need CN/OOT ever again (although they are good to have as a backup plan)