The only way to send data through Nintendo Ds emulator is via the Download play menu, apart than that it's just some technical data that nobody used. Though, I think there's no program to manage data between the computer and Nintendo DS emulators.
This was all done with Pokemon Black and Pokemon White both on Nintendo ds emulators. Although it's nearly not possible to trade using Wifi or more precisely the Friend Codes, some people believe it's possible through a WIRED connection.
