Well yeah a save manager would work, but what wrong with just having two games? Only problem is remembering which one has the right file for each user. Or use two different sd cards.
Messing with save manager can sometimes have mistakes like overwriting files and messing things up, so be careful, Swapping sd cards (IF YOUR NOT USING NEW 3DS) Is as easy as switching games since it basically the same thing.
Then again nintendo never intended for any pokemon player to have more than one save file on one system for 2 different players. So there is that....