Pokewalker won't work with the Rom. You have to use the real game cart, which has a built in IR Port.
No im talking about the actual game. If i make a file, then transfer my starting pokemon to my pokewalker and then start a new game, will i be able to transfer that pokemon from the pokewalker to the new game?
Well what I think would happen is: That once you delete your old save file and start a new game the Pokewalker will reset. But you can try.
like john said you can try or send it to yours or a friends game instead. idk but the same thing may happen with the pokewalker as what happens with the Pokemon Ranch for Wii: when you reset your game you can't retrieve your pokemon. no idea if this is the same situation though
actually no it doesn't work that way. once you use a pokewalker on one game it locks it to that game. but if you want to you can reset the pokewalker so it can work with another game but it wont keep a pokemon you want to transfer, you have to trade it the old fashioned way.