So once the species/gender have been generated, it's just like any other stationary, using the Hidden Hollow PID frames? How do I control what is generated?
Edit: do the pokemon's bobbing movements advance frames?
Once the species/gender has been generated it's a Hidden Hollow encounter type. Set your encounter type in reporter to Hidden Hollow.
Basic guide to control what is generated:
1) Find out which hidden hollows before it are empty/have nothing in it. If you need help with the numbers check here and know the first one listed is 0 and the last one is 19.
https://dl.dropbox.com/u/12206225/hollow.htm
2) From that same list find what slot/subslot you need for the Pokemon/Item you want. Pokemon are slots 0-2. Subslots are the letters at the top. 0=A, 1=B, 2=C, 3=D.
3) In reporter enter all the information you gathered. Number of open hollows are the number open. Advances are how many advances you want (I generally do 3 just so I can verify the seed with chatots). Hollow number is the sequential number of the desired hidden hollow based on the number of open hollows. Example:
I have Route 5, Route 7, Route 9, Giant Chasm, Route 22, and Route 2 open.
I want to abuse Giant Chasm so I enter 6 as the number of open hollows and 3 as the desired Hollow Number (count from 0).
Slot is whatever slots you want. Subslot is whatever sub slots you want (generally all of them are fine).
For the same example say I want a Ditto. I'd enter Slot 0 and don't care about the subslots.
If I had wanted a Seviper on Route 7 on White2 I'd have entered 2 as my slot and 2-3 as my subslots.
If you care about gender just look at the gender ratios on that sheet and see if the gender you desire is at that specific ratio in reporter. Later I'll add gender filters for the seeds.
4) Save inside the hollow you want to abuse.
5) Hit your seed.
6) Advance/verify with Chatots if needed.
7) Walk 256 steps (you can go over, just at least 256 steps). Since it doesn't matter if I go over I just run around for a while. You could spray a max repel and then do 6 extra steps after that.
8) Exit and reenter the Hollow.
9) Save in front of the Pokemon.
10) Search in reporter for a seed with the desired IVs. (Frame 1 is best and not that hard to find but you can do a search of 1-6 if you're fine advancing the IVRNG frame).
11) Enter that seed in the main window and search the PIDRNG with the Hidden Hollow encounter type to find a frame with the desired Nature.
12) Hit the seed, advance/verify. Catch your Pokemon.