In my idea, if you already record stats, adding bonuses will be easy. You'll just have to watch the stats after the game.
The "maths" will be simple. Believe me, I'm not a math brain, far from it.
Just have to find a easy and fair formula for each important position.
For the next game, it will be simple, the linemen and strong positions will be weighted, you'll just have to watch your experience sheet to see wich athlete has a bonus or not,
after the completion of a play. You RB is tackled, your QB has already throwed the ball (=ball marker is on the field), you just have to read the experience sheet to see if your RB or WR has extra yards.
The key is to add bonuses on play completions. If the athelete does not throw/carry/recieve the ball, you change nothing to the system.
The weak part of it, it's how to manage bonuses on defense, and for the QB. But we just have to think about it.