When Jeff Moorad became the Padres' CEO last month, he immediately empowered general manager Kevin Towers as his decision maker in the baseball operations department. The choice follows the same model Moorad employed as the Arizona Diamondbacks' CEO for the previous four seasons.

And while the method in which the Padres' front office now operates is familiar for Moorad, it is vastly different for the Padres, and that's a good thing, sources say. Moorad's move has added a level of clarity to the decision-making process that many sources familiar with the organization said was muddled under former CEO Sandy Alderson.

For Moorad, however, the decision was about making things clear and easy.

"It streamlines the process," Moorad said. "It makes reporting channels unambiguous, and at the end of the day, I think, makes for a clearer-thinking organization."

It's not that the Padres were devoid of thought under Alderson. To the contrary, sources said, the Padres thoroughly thought out any and all decisions, looking at each from various perspectives. Many around baseball believe the Padres might have been overthinking their options.

That ultimately may be why the Padres failed to trade ace pitcher Jake Peavy over the winter. Talks broke down with the Atlanta Braves last November and negotiations with the Chicago Cubs met the same fate a month later because, one source acknowledged, the Padres routinely asked for different packages of players and couldn't agree upon one.

The delay in the decision-making process reportedly upset Atlanta GM Frank Wren to the point where he ended talks. It also kept Peavy in an uncomfortable state of flux throughout the winter.

"We've had a lot of cooks in the kitchen, no doubt," said one front office source who spoke on condition of anonymity. "It's always been organized or tried to be organized so that everybody is in the loop, so that everybody was a piece of it. But sometimes we're all going our own different ways. Has it become confusing? In some situations."

One baseball source said the team's decision to offer Peavy his contract extension in December 2007 was a minority decision. At the time, the Padres formulated three options -- trade Peavy, allow him to become a free agent after the 2008 season or work toward a multi-year contract extension.

Ultimately, Peavy signed an extension through 2013, a deal that guarantees him $52 million after the 2009 season.

"There were strong supporters of each position in the hierarchy," the source said. "And getting the deal done was the minority position."

The team was also divided over whether to retain free agent center fielder Mike Cameron after the 2007 season. Ultimately, the Padres traded for center fielder Jim Edmonds and let Cameron leave as a free agent, a move that backfired when Edmonds struggled and was released on May. 9.

There was also a split over whether or not to re-sign free agent closer Trevor Hoffman, who left for Milwaukee in January after each side publicly criticized the other.

Often, when he was asked about baseball decisions, Alderson directed questions to Towers. As Alderson said last season, Towers was the GM, and "ultimately, he's the one who makes the final call." But several front office sources, all of whom spoke on condition of anonymity, said executive vice president Paul DePodesta directly reported to Alderson, a decision that made Towers uneasy because he wondered if he was being second-guessed.

One front office source downplayed that suggestion, saying over the winter: "nobody thinks Paul is walking around believing he's going to be the next GM."

Another source, however, said the choice caused mistrust and pitted DePodesta's opinions against Towers'.

"When you've got somebody involved in baseball operations who reports to the CEO," the source said, "does he have (power) to go to the CEO to say I wouldn't do it?"

Another source said the questioning of the decision-making process became more common after the Padres lost 99 games last season, saying that it was functional in previous seasons.

"Has there been conflict on opinions? Yeah," the source said. "But isn't that supposed to be a good thing? That's what makes great baseball, and at some point Kevin makes the decision."

For the time being, Towers is the only decision maker, and he reports directly to Moorad. Towers will continue to gather information from all the sources within the Padres' front office and use it to make the decisions he sees fit.

And that's how Moorad prefers it.

"I believe in openness," Moorad said. "I believe in hiring the best class of talent and letting them do their job and giving them the autonomy to do their job, but at the same time holding them to a bottom-line standard that's relevant and appropriate."

Contact staff writer Dan Hayes at dhayes@nctimes.com. For instant coverage, follow the Padres at twitter.com/nctsports.