Warner, now an analyst for NFL Network, offered a summary of his work with Kaepernick on NFL Total Access on Wednesday.
"What I love first and foremost that's Colin's working hard," Warner said. " ... The hard thing is that you're taking a guy who has relied so much on his athletic ability over the years and you're trying to turn him into a guy who can be more comfortable in a quarterback position."
Warner said things were simpler when he was a player because he had less athletic ability than Kaepernick. "All I had to do was play quarterback," Warner explained.
"For (Kaepernick), it's finding that balance between 'When do I be a quarterback?' and 'When do I be an athlete?' And trying to find that mix between the two," Warner said. "... So the real question is going to be, when the bullets are flying and guys are chasing after him does he revert back to being an athlete or have we made some progress in making him more of a quarterback and staying in a quarterback-friendly position to be able to make more consistent, accurate throws down the field."
Kaepernick, 27, set career highs in passing yards and rushing yards last season, but saw most relevant statistical numbers fall off in his second full year as starter. Kaepernick posted a career-low passer rating of 86.4 and averaged just 7.0 yards per attempt.
The 49ers, meanwhile, quietly locked into another year with Kaepernick this week. The quarterback's $10.4 million base salary for 2015 became fully guaranteed Wednesday, according to CSNBayArea.com. Kaepernick's 2016 salary will be about $14 million, a figure that might give the team pause if progress is not made.