"That’s the role that he’s been in since he’s got here," Harbaugh said on Tuesday. "He’s doing very well, picking up the system. And a guy that is really serious and focused on being good and doing a good job. He’s got a lot of things that motivate him to work hard."
McCoy realizes nothing is set in stone. His grasp of San Francisco’s No. 2 quarterback job is not complete.
"I feel like I'm doing well with the 2s," McCoy said. "Still, I have a lot of room for improvement. There's good things and bad things at practice every day."
Learning San Francisco’s offense has been a challenge for McCoy, who is picking up his fourth offensive system in four seasons following a three-year stint to start his career in in Cleveland. The 49ers, however, are already in the latter stages of offensive installation with starting quarterback
"If we're reading a book, we're at the end of the book," McCoy said. "Every day presents a unique challenge for me. Just really trying to soak it all in and compete when I'm at practice."
While there are some similarities to the West Coast offensive schemes he ran in Cleveland, San Francisco's system provides a whole new set of challenges. Mostly, it’s the 49ers quarterback-driven running game.
Working out of a shotgun formation isn't a new concept for McCoy, who ran zone-read plays at the University of Texas. McCoy, however, has asked Kaepernick questions during practice to better understand the nuances of the team’s “Pistol” scheme.
"Kap's helped a lot," McCoy said. "That's a little bit new. The pass game, I think that's coming along. I just really have to continue to stay focused. I'm a competitor. When I'm at practice, I want it to work. I want to do it right."
McCoy showed his strides in the passing game by connecting on several deep passes to his tight ends during Tuesday’s Organized Team Activity at 49ers headquarters. McCoy found
OTAs allow McCoy the opportunity to prepare like he’s in a game, but he’s still not finished mastering his new offense.
Having played against the 49ers in 2011, McCoy had familiarity with the team's personnel, but he has been even more impressed with the talent on the roster after seeing it up close on the practice fields in Santa Clara.
"Vernon is fast," McCoy said after the same practice he found the starting tight end for a 40-yard touchdown pass. "He is definitely a weapon on offense that we can use in a lot of different ways. I can't say that I've ever played with anybody like that. When he's out on the field and you're reading your progressions, in the back of your mind, always know where Vernon is."
With weapons at his disposal, McCoy said the 49ers have the ability to be an even more explosive team in 2013.
"I haven't played any games yet in this system, but we have the potential to do a lot of things,” he said.