Afaik, Gateway is the only way to backup your NAND so yes, you'll need to delete your CN save and scan the Gateway QR (then do the same again to get Ninjhax back up and running).
Have you looked into ReiNAND? That's what I'm currently using. It has emunand support (upto 9.5 for N3DS), plus the latest build can actually boot using the MSET exploit, so no need to carry a copy of Cubic Ninja.
Alright thanks, this is what I'll end up doing before installing any other CIAs or anything else.
When I was deciding which route to take regarding CFW I did look into ReiNAND, but at that time it looked a little complicated and I was reading about quite a few complaints about it being unstable. Seemed like the best way to go was Pasta for now, and hold out until RX w/Pasta gets N3DS support. But maybe I'll read a little more about the latest ReiNAND release and go from there. Is three really a great chance of bricking my N3DS just installing game CIAs, and maybe a theme, to my sysNAND?
Who knows, maybe down the road I'll even end up buying a Gateway (if I can find one used for cheap) and try that. I'm thinking about doing a hardmod, just to have, maybe sometime down the road too.
If I do end up installing RieNAND instead, or Rx w/Pasta, will I have to format everything and re-install all my game CIAs? If so, can I restore my gamesaves somehow?
Sorry for all the questions guys, but thank you everyone for taking time out to give me some great answers. This community is amazing!