ReiNAND CFW and Pasta CFW are currently the choices for CFW on the N3DS. I would go with ReiNAND as it has emuNAND support. You will need Cubic Ninja or a Sky3DS with Cubic Ninja installed to run it the first time. After the first time, you can downgrade your N3DS's MSET and launch ReiNAND through the DS profile exploit.
I would set up rxTools CFW. It has support for the latest emuNAND version and a lot of other functions that Pasta does not. Everything should still work fine once you move on to emuNAND. If for some reason the saves don't transfer onto emuNAND, you can extract the saves from sysNAND and inject the saves into emuNAND using SaveDataFiler.