I’m gonna open this up to any FRINGE fans out there, as I love the show, but am not familiar with how exactly Nielsen ratings work. I did, however find some info on your question in the comments of this post. It was mentioned there more than once that DVR’d re-watches count as a viewing in ratings. So basically, watch it live, then re-watch your recording of that episode within three days of recording it, and each viewing will count as a separate viewer. The catch being, you can’t fast-forward through commercials when you watch the recording (something about helping out the advertisers). I hadn’t heard about the whole Nielsen box rule, and have never known anyone to have one; according to one comment there’s only like 50,000 some odd boxes out there, so…that’s not really a good ratings system if true.
In terms of whom to contact, I’m not the best person to ask this, sorry. I’m not as “involved”. If you’re on Twitter, help it trend on Friday nights. There are a few sites that get certain hashtags going every week. I know the executive producers are on there, too.
EDIT: another reply for you in the notes, anon.