The 49ers raised their contract offer to quarterback Alex Smith only "moderately" in late negotiations, a league source told CSNBayArea.com on Wednesday.Smith signed a three-year, 24 million contract that includes 9 million in fully guaranteed money, the source said. If Smith maxes out his incentive package -- likely based on play time and undisclosed performance levels -- the total package of the contract can reach 33 million.The total money available to Smith in his contract did not change from the 49ers' initial offer several weeks ago, the source said. But the 49ers did raise the guaranteed money 1 million from their initial 8 million offer, according to the source.Smith said on Wednesday that coach Jim Harbaugh and general manager Trent Baalke informed him last week of the club's interest in free-agent Peyton Manning. Smith said he was not offended that Harbaugh and offensive coordinator Greg Roman flew cross country to watch Manning work out.When Smith remained unsigned through the first five days of free agency, he took a visit to meet Miami Dolphins coaches and team officials on Sunday. During that time, the 49ers never took their offer off the table while the club pursued Manning, Smith confirmed.Smith's option began to dry up over the weekend when the Seattle Seahawks signed free-agent quarterback Matt Flynn. Then, the Dolphins signed former Jacksonville starter David Garrard, awarding him a 1 million signing bonus.After Manning chose the Denver Broncos over the 49ers and Tennessee Titans on Monday, the 49ers raised their offer of guaranteed money to Smith by 1 million, the source said.Smith said in a conference call with reporters on Wednesday that he was not upset with the 49ers' offer of years and commitment."The issues came more from the structure than anything," Smith said. "Really, the money wasn't an issue. Those of you guys who know me know what type of guy I am. Money is great for security, but I'm not the type of guy who has a bunch of flashy cars. Other than taking care of my family, it's not something that means a lot to me."And, really, just a matter of working out the structure of the contract to get it to where we felt good about it."Agent Tom Condon, working on behalf of Smith, and 49ers chief operating officer Paraag Marathe negotiated the deal. In the end, Smith said he returned to the only place he wanted to play in 2012."For me, this was the plan all along," Smith said. "Obviously, since the season ended, I wanted to be back here. And it dragged out a little bit, but glad it's over. Glad it's done. I'm glad to get back to work."