Football is a sport that requires a ton of explosive movement and a lot of speed. At virtually every position and at every level, speed is what separates the men from the boys. QB, offensive line and defensive tackles are the exception.
So as far as working out goes, I would highly recommend a LOT of explosive movements like the snatch, cleans, jumping squats and a lot of explosive pressing from various angles. And a LOT of sprinting. Your kid, at his height, will probably end up around 6'4"-6'6" by the end of his senior year, which would make him an ideal candidate for QB, WR or TE, or maybe defensive end if he fills out.
So I'd get him throwing and catching the ball as often as possible now. When doing sprint work, I'd have him do a lot of stop/start stuff, changing directions, running sideways with crossover steps, and a lot of jumping in various directions. He'll have to have good hips and quick feet.
I'd turn him onto this site as well, and steer him toward Thibadeau's "Look Like a Bodybuilder, Perform Like an Athlete" article and his neural charge series of articles. This stuff isn't that much different than what I used to do in high school football and his "Bodybuilder/Athlete" program never forces him above about 80% of his 1rm, which is nice since he won't be used to handling relatively large loads yet.
Also, I lift with a couple of taller lifters on occasion (6'2"-6'4") and I myself have pretty long arms and legs for my height (6'1"), and I've found that all of us see better results lifting in a lower rep/higher set range on a regular basis. I've heard that this is the case for most "taller" lifters, so this is another reason why I think Thibadeau's program will be good for him.
It has him doing a lot of upper-body pressing, which is a big focus of most football weight programs, and he'll be doing roughly 20-25 sets of 3 reps. For the lower body days, he can use the Oly lifts. I'd recommend he do front squats and snatches. Snatches are one of the best overall exercises for developing explosive strength, which he'll need for football, and the front squat really hammers the quads. The quads are the primary muscles used for acceleration, and again, this is a key aspect of success in football that you can help him work on.
As far as skills go, catching the ball is clearly going to be important, as will throwing the ball if he wants to play QB. So get him playing catch as much as possible. And route-running will be key as well, so get him running routes and working hard on coming into and out of his breaks. I wouldn't worry about building up endurance yet. They'll take care of that during two-a-days. I'd focus more on basic skills and building up his strength. Get him a Prowler for his conditioning.
Now that I've written a book here, hope this info serves you guys well.