Just post it as a new post in the contest thread whenever you're finished. You may wish to put it inside of spoiler tags, but that's not necessary. Just keep in mind that you lose points if you have to edit your story after posting it so make sure everything is complete and double-checked before posting!
Hey. Regarding Pokegen, I just wanted to let you know that I'd really rather not download a program that I have never used before and will almost definitely never use again solely for this purpose.
Regardless, I'm sure that you will find plenty of people who do have it and will be willing to help you.