A GM has a long and complicated job to do in July. He first has to assess his team's needs which change on a daily basis because of injury, rookie emergence and waiver wire additions. He then has to gauge the talent being offered around the league. He then has to evaluate his prospects and mark some off limits. After, he has to call GMs around the league to either court offers for a player or ask about certain players. You then have to match up the prospects and the money alongside he centerpiece of the deal and walla you have your trade.
Sometimes a trade like the Manny trade happens, where a team has to pays extra because of the fact that they have to expose of a certain player who's corroding their clubhouse and identity. So instead of making a fair trade the Red Sox traded the superior player along with two prospects and $7M for a season and a half of the inferior Jason Bay. The Red Sox are in some ways repeating 2004, where they traded the superior Nomar Garciaparra for the inferior Orlando Cabrera but somehow managed to win the World Series. How did this work? Because Theo Epstein is a genius. He figured that although Nomar was the superior player he was extremely injury prone meaning that 30%-40% of the Red Sox performance at SS that year was coming from Pokey Reese. Orlando Cabrera easily trumped 40% Pokey Reese and 60% Nomar, therefore the trade strengthened the Red Sox. In Manny's case, he never gave 100%, he was destroying the clubhouse and was ditching important baseball games. Jason Bay at least equals this level of performance if not trumps it. Jason Bay is not that far behind Manny statistically and all in all he's a better fit for the current Red Sox therefore giving the Red Sox the advantage and not the disadvantage. These are the kind of things that make Theo Epstein a genius.