whose theory it is?
“About that digging in the basement.”
“What about it?”
“That’s a hell of a trench down there.” Corbett waited a beat, but Eli didn’t respond. “No clue who’s responsible?”
“If I had a clue I’d have told Deputy Hanson.”
“It’s his theory and, I’m told, yours, that whoever broke in the night Duncan was killed dug it. And since he sure as hell didn’t do all that in one night, it wasn’t the first time he’d gotten in.”
“It’s a theory.”does "“It’s his theory and, I’m told, yours"= "he told me your theory, that is..."

Question

whose theory it is?
“About that digging in the basement.” 
“What about it?” 
“That’s a hell of a trench down there.” Corbett waited a beat, but Eli didn’t respond. “No clue who’s responsible?” 
“If I had a clue I’d have told Deputy Hanson.” 
“It’s his theory and, I’m told, yours, that whoever broke in the night Duncan was killed dug it. And since he sure as hell didn’t do all that in one night, it wasn’t the first time he’d gotten in.” 
“It’s a theory.”does "“It’s his theory and, I’m told, yours"= "he told me your theory, that is..."

Answer

It means that Corbett thinks that it's Deputy Hanson's theory, and believes [ "I'm told " ] also, that it is Eli's [ "yours" ], that the trench had been dug by whoever had broken in on the night that Duncan was killed.