I'm playing the adventure with the same angle (Ned as a Brotherhood Spy). Here's how I'm playing it:
1-2 years ago: Skerrin and the other Brotherhood agents in Saltmarsh have found out that Gellan Primewater secretly does business with the Sea Princes. They start hatching a plan to reveal this to the public without bringing any attention to the Brotherhood.
some months ago: Skerrin finds out that Sanbalet's Gang (who have dealings with both Gellan Brimewater and the Sea Princes) have established their base of operations in the haunted house. He sends Ned in as a spy to infiltrate the gang.
Ned joins Sanbalet's Gang (basically in deep cover), waiting for a signal from Skerrin.
Meanwhile, the other Brotherhood agents in Saltmarsh manipulate the poacher to check out the house by mentioning the treasures that are surely to be found within.
Some days ago, the plan finally pays off. The poacher checks out the house, is scared off by Sanbalet's magic (just like the Brotherhood expected) and returns to town to tell the authorities about this (also just like the Brotherhood expected).
Skerrin manipulates Anders to hire some adventurers to vanquish the evil undead in the haunted house, then he contacts Ned (through whatever means of communication they have) that the time has come.
Ned, volunteering for watch duty on the upper floor waits for the adventurers to show up, then drops his belongings in the storage room, locks himself in the bedroom, gags himself and ties himself up (which is something he can do apparently). Then, when he hears the adventurers enter the house, he makes some noise to draw attention to himself.
Ned's fake story is the same as the one described in the book: He's a traveler on his way to Saltmarsh who was knocked out by unknown attackers in this house. But his goal is to make sure that the adventures find out about Gellan's involvement with Sanbalet and his gang. So unlike what it says in the book, Ned will not try do dissuade or hinder the plays, he will actually help them along, giving subtle hints and making sure that they find all the necessary clues (without giving away the game of course).
So he will want to tag along, but at the same time he needs to make sure that none of Sanbalet's gang see him (because they would of course recognize him and thereby tip the players off that his story about being a traveler is a lie). And the answer to how he does that is the answer to how I play him:
He acts like a coward. He refuses to leave the players because he's too afraid to continue travelling to Saltmarsh by himself. And he won't join the players in any of the fights because he doesn't know how to fight. So while the players take out everyone of Sanbalet's gang, he just stays behind and only shows his face again after the fight is over.
It's stupid, it's convoluted, but hey, it sounded to me like a lot of fun. :)