How exactly do I make the alternate save file? I figure I should ask before playing around, don't wanna lose my save game now, it would be a really depressing way to end the game haha
Yes they will appear later as you finish the game... Once you get Arceus most legendaries will be available.
You have a save folder where you can store save files in case you want to play an alternate. But I'd just copy the entire folder so you can have a "copied" version where you can restart. Then you have your original in one folder and your new in the other.
Here is my Ivysaur
and here is the confirmation code
I'll trade back so your pokemon can evolve
BTW you can talk trades and stuff in this thread: http://www.pokecommunity.com/showthread.php?t=207320&page=6