from what it sounds like your nands are linked. to tell for sure In your SD card, there should be a Nintendo 3DS folder. Open it,
the folder inside that (has a long name of random numbers and letters). if there are two of these you are likely unlinked
there are many reasons to unlink nands most notable at the moment is to use themehax to boot cfw from a cold boot (requires sysnand 9.0/9.2)
https://m.youtube.com/watch?feature=youtu.be&v=LcAMVMpXjzo as well as downgrading whitelist to re-allow old once blocked ds flashcards ex: ak2i
the only real benefit of linked nands is the fact that you can install gba and dsiware on sysnand and play them from emunand without needing to install them to emunand also there are sometimes bugs associated with linked nands like apps re-wrapping themselves
it will write its own mset over that one if you want, but after the initial install the best way to load cfw is themehax
https://m.youtube.com/watch?feature=youtu.be&v=LcAMVMpXjzo (works on n3ds as well)
also if you have cubic ninja, you can use that for the install instead of browserhax durring initail instalation as some users have problems getting browserhax to work