I've done Stay and Scream for the past two years.
For 2005, we were there for opening night and stayed at Islands of Adventure (as
HHN was held mainly in IoA, with only the sound stages at the Studios involved). They put us in a "holding area" that was in a back lot area between the two parks. They set up games and food vendors. During the event, this area served as the passage way to two of the haunted houses in the sound stages. I can't remember exactly where it was, but about an hour before they let people in, they had the route clearly marked. I must admit, it was a bit of a bummer because a line formed and there was no place to sit. We sat on the ground because we were getting tired from being at the park since 8:30AM. We didn't want to get off the line to get food because we'd lose our spot. Regardless, the wait was worth it because we got into two of the haunted houses IMMEDIATELY.
Last year we had a more pleasant experience because HHN was held solely at the Studios and we did the Stay and Scream there. They had a holding area in the NY area of the park close to Finnegan's pub. We decided to eat at Finnegan's and it was nice to be in the air conditioning! We're planning to do the same again this year, if it's the same set up.
The holding areas always seem like a huge secret for some reason. Half the workers the day of always seem to be clueless. We even had a couple of them tell us that there were no holding areas! Guest relations even seemed confused and suggested that we just "look around for people taking tickets and handing out bracelets". We finally asked around enough and got a straight answer. Hopefully we only encountered this because we have always attended opening night.
You guys should have enough time to ride the attractions at IoA. I think they only let us line up about an hour before HHN began.
This year, we just plan on asking until we get some correct information and plan on heading to the holding area. No matter what it is, it will be worth it to "Stay and Scream", because we have always been able to get through all the haunted houses except for our last one with a 20 min or less wait. It always seems like we get stuck waiting for the final one of the night. It's easy to be patient though, after breezing through all the other haunted houses!
I will be going opening weekend, so I will try to post the info I can find out afterwards.