@johndpoe yes, and no it does alter N3DS's system settings aka MSET.
you'll find the detailed process on the Gateway's website, but i'll summarize the steps :
1) Add Cubic Ninja to sky3ds, and Gateway's launcher.dat at the root of your N3DS µSD card.
2) Connect the N3DS to a router with internet access (from this step, never put your N3DS in sleep mode or it will download the 9.9 update in background !)
3) insert sky3ds, toggle to Cubic Ninja with the blue(or red) button, launch it, select QR Code and scan Gateway's 9.0E QR Code, it'll bring you to the Gateway menu.
4) Begin with a NAND backup, then hen finished press B and dpad down to shutdown the N3DS.
5) eject your N3DS µSD and copy the NAND.bin to a safe place, and keep it SAFE ! In case of brick, you can recover with a hardmod and that file. Also, backup every folder on your N3DS.
6) Insert back the µSD in the N3DS, turn it up, go delete the internet connection to make sure it won't download anything (tip : create 3 fakes connection, that way your NAND will remain safe from an unwanted connection).
7) Launch CN (Cubic Ninja), go to QR Code, Gateway menu pops up, select "format EmuNAND" : it will wipe your SD (that's why we made a backup at 5)
). When finished, turn off N3DS with B and dpad down again.
8) Turn on the N3DS, go to settings and format N3DS. Now, your SysNAND and your EmuNAND are unlinked. Turn off again, put backup back on µSD (NAND.bin not needed), make sure Launcher.dat is present at the root, add also mset_eur.cia that you'll find in Gateway's archive, then insert back µSD and turn N3DS on.
9) Now, we'll need the GW red card. You will need to find on Google DevMenu.3ds (MD5 : E65629FBE2AE8A419CF8624DF78E78B2) and put it on the GW's µSD.
10) Launch CN, go to QR Code, Gateway menu pops up, select Boot Gateway mode, hold B and press A, then insert GW Red card and press X. You'll end up on your SysNAND, press select, choose DevMenu, launch it as a game card, select SDMC, broswe down to mset_eur.cia and press install it. (optional : if you want to use the GW blue card, install bluecardfix.cia the same way). Once done, click home button then X, turn off your 3DS and turn it on again.
11) Now, on your R4i Gold (or GW Blue card if you installed the fix) put GW_INSTALLER.nds (it's in folder Blue Card R4i), then launch it as a game and install MSET. If it doesn't work, you can do it via GW Menu with Cubic Ninja. From now on, you shouldn't have to use CN anymore. To launch GW, go to settings, profile then DS profile will launch GW menu ! Note after playing a DS game, it may erase the payload, simply run GW_INSTALLER.nds again to restore it
Hope it'll help you out !