Hugh Freeze doesn’t have this thing figured out yet here at Auburn. It’s only been three games, only one of them against a Power 5 opponent. Growing pains as he installs his own offense are all part of this process and boy, Freeze has sure made a point to list them.

There have been penalties and poor alignments. Patternless quarterback rotations, players running the wrong way and play calls that haven’t made a whole lot of sense.

This night — Homecoming, a full Jordan-Hare Stadium and a game against Samford — marked Auburn’s final tune-up game before SEC play, and Freeze’s plan was clear. He had questions to answer. Many of them centered around his quarterbacks and a passing game that had failed as a team to pass for a total of 300 yards combined across Auburn’s first two games.

“Just wanted to be balanced, really, and get us some confidence,” Freeze said after the 45-13 win over Samford. “We’re going to have to throw the football some, and they were playing — the way their safeties were playing, they were getting eight in the box really quick. A lot of those throws in the first half were truly off the run game. But the read for Payton was to throw it based on the numbers.”

So Auburn came out ready to throw. A lot. Probably too much, actually.

Quarterback Payton Thorne dropped back to throw on 12 of Auburn’s first 15 plays. He kept it himself for a scramble on two plays and threw the other 10. Auburn efficiently moved the ball on what at that point was possibly Auburn’s best all-around drive in two weeks.

Then the Tigers got all the way down to the Samford one-yard line. The questions returned.

In previous games, this was the situation where Auburn would look to either backup quarterback Robby Ashford or someone in the running back room that Freeze has been so keen to lean on.

Auburn did neither.

Thorne had an incompletion to Jay Fair on first down, and an incompletion to Shane Hooks on second down. Auburn appeared to line up for what looked like a running play on third down, but then came one of the mistakes that cost Auburn dearly a week ago against Cal: penalties.

Izavion Miller was called for a false start and pushed Auburn back to the six-yard-line. Auburn had to throw, and Thorne tossed an ill-advised pass that ended up as an interception.

“We go to third down then we had a false start or something, I don’t know what it was, moved us back a little bit,” Thorne said. “I’ll have to go look at it a little bit. Maybe I ought to have thrown that away.”

Late in the first half, Auburn drove down inside the Samford 10-yard line again, and yet again threw the ball three straight times. After a loss of yards on a screen to Jeremiah Cobb and two incompletions, Auburn kicked a field goal.

That’s two first-half drives right on the doorstep of the endzone and three total points.

“It kind of worked out that way,” Thorne said of all the passing plays. “We call an RPO, so possibly to hand it off or throw it. I thought I had the look for the throw.”

First-half mistakes also featured a second Thorne interception on a poor decision of a pass thrown into double coverage. When Auburn did try to run the ball on a short-yardage fourth down play near midfield in the first half, Damari Alston was stuffed at the line of scrimmage.

Auburn had five penalties total — four of them in the first half. An improvement from the Cal game, but still costly.

The heavy lean on the pass throughout the first half fulfilled Freeze’s plan to find Thorne some confidence. In the first two games combined, Thorne had 19 completions for 235 yards. In the first half alone against Samford, he had 18 completions for 232 yards.

“I thought Payton was solid outside the one decision on the deep post route,” Freeze said. “That was a poor decision. But outside of that, I thought his decision-making was pretty good. I thought he ran when he needed to. We called some good draws with him, and he looked normal running those.”

The passing numbers don’t indicate the difficulty Auburn had to pull away in the first half. Auburn didn’t score at all in the first quarter.

It also created a situation where while Freeze got what he wanted with Thorne, he wasn’t able to get Robby Ashford in the game the way he’d also discussed. It’s hard to get both players on the field while also keeping rhythm for either. Ashford didn’t play at all in the first half.

It’s another growing pain. Auburn figured out part of the offense against Samford. But how it will get the whole picture involved will be an ongoing change.

“We’ve got to find out if Payton truly is going to function every aspect of the offense, which I thought he did tonight well,” Freeze said. “It’s good to have both of them. How that looks from game to game? I’ve said from Day 1, I don’t know. We’ll have a good plan going into A&M. And I’m sure it will involve both of them.”

After halftime, things changed. Auburn fixed flaws found on the offensive line. Ashford was added back into the game plan. And Thorne became the balanced quarterback Auburn has been looking for.

Auburn pulled away.

Throughout the preseason, Freeze has critiqued Thorne’s decision-making, but nearly always that centered around his choices in Auburn’s run-pass-option offense.

He made many better decisions in the second half of this game, especially with regard to keeping the ball himself. It led to 123 rushing yards — the most of any Auburn quarterback in a decade.

“I guess I’m not that slow,” Thorne said.

Matt Cohen covers Auburn sports for AL.com. You can follow him on Twitter at @Matt_Cohen_ or email him at [email protected]