"Checking the plumbing and keeping the trains running on time really is what the DNI is doing, and the president is looking elsewhere for that final, critical, definitive intelligence advice," the official said.
Will that advice come predominantly from Brennan, who has had such open access to the president, rather than Clapper, effectively bypassing him?
Jones, who has worked firsthand with both Brennan and Clapper, doesn't foresee any real turf battles, even though the two men will not always agree.
"John Brennan and Gen. Clapper are two of the most consummate professionals I have ever worked with," said Jones, a former national security adviser to Obama. He believes "they will work hand-in-glove together."
The two men do have a history of working together in the intelligence community, especially over the past four years.
"Every indication I've ever had is that they like and respect each other," Townsend said, adding she was unaware of any major disagreement between them.
When asked by CNN if Clapper believed his authority as head of the intelligence community would be in any way compromised by Brennan being CIA chief, DNI spokesman Shawn Turner said: "Director Clapper leads the intelligence community, and he's always had great relationships with the directors of the (other) agencies, especially the CIA. That will not change when John is at the helm at the agency. He and the DNI are longtime friends and colleagues. They have always trusted and respected each other in their respective roles and I'm confident that will continue to be the case."
And the bottom-line, according to Townsend, is not whether the national intelligence director or CIA director is considered the president's senior intelligence adviser; every president will have his own model.
It's about getting the job done, and providing the president with accurate, timely and effective advice.
"If you make it about the mission and where the capability lies, and these two guys put their egos aside, then you ought to be OK," Townsend said.
And Jones said that's what these two will do. "It's not about them. These are two people whose egos are completely in check."