Yes you can. However you need some special hardware.
First you need a Flashcart. A flash cart is an special cartridge which allows the use of homebrew in the DS. Homebrew software is software developed by the community to be used on certain device or environment. This homebrew usually comes in the form of roms or similar.
With that said, you can use such a Flashcart to load a .rom into it, and then use your DS with that cartridge to launch the .rom. Now given that you already have a save file you want to transfer, you need to copy the save file to the Flashcart too, these files are usually placed besides the rom, by the respective emulator.
Now, following this process you cannot transfer the pokemon between your Flashcart and the X and Y games, because of some security measures implemented by Nintendo. So you need to transfer them to a previous generation game first. Which is great given that you do have the Black cartridge.
So, to transfer the pokemon between the two Black versions you need two DS with the respective cartridges, and use the Union Room to transfer the pokemon.
Once you got your pokemon into the real cartridge, you can transfer them to X and Y using Pokemon Bank.
Note: I have not done the process myself, but some time ago, I was thinking about getting X and Y, and looked up about the transfer possibilities. And i read some tutorials explaining what I stated above.