I suppose everything will be fine, since you have two cartridges. The game should save on the cartridge, so they'll be completely separate files, towns.
I suppose.
I only have one digital copy, but maybe one of the cyclers can answer this question for you =)
Just be warned that if you want to transfer anything from one town to another, you'll have to go through a friend. I really wish the online was set up more like City Folk's....