3DS New Leaf File?

I have two Nintendo 3DS consoles, and one copy of Animal Crossing New Leaf. I have a town on the first 3DS, but what I fear is that if I put the cartridge in the other 3DS it'll corrupt my save file. The first 3DS has an SD card but the other one doesn't.

If I play the same New Leaf copy on either 3DS console, will the game have separate save files so that I won't corrupt my main file?

All (non-digital-download) Animal Crossing New Leaf save data is stored on the cartridge, switching the cartridge between different 3DS consoles will not corrupt your savegame data, and both consoles will load the same save file.

The only thing that may change by switching the game between 3DS consoles is some online data, as (I believe) the game uses the system's friendcodes. So you may need to re-register friendcodes on the new system (and have said friends add your second 3DS's friendcode). Streetpass data is also saved to the system, But that (should) only affect pending streetpasses that you haven't claimed the rewards for yet.