I do use a formula, but I also make some adjustments when I feel they are needed. My current formula for QBs is based on statistics from that season.
Short Accuracy= Completion %+29
For medium I take the yards per attempt and create a new number. 10-yards per attempt example: if a QB has a yards per attempt of 6.5, I take 10-6.5=3.5 I then use this number(10-Y/A) and subtract it from the Short Accuracy.
Deep Accuracy, I use a similar process except I use 20-yards per catch.
example: yards per catch is 11, I take 20-11=9 I then take that number away from the Short Accuracy.
This year, because of the revamped attributes by EA, especially in terms of DAC, I ended up subtracting an additional 5 to 7.
The process is not perfect, but it seems to work.
For awareness I use the following for QBs: 15+(Exp*3)+gamesplayed+(games started*3)+TD%-INT%-SCK%
Again, not perfect, but it seems to work. Like I said, I also make adjustments as I feel they need to be made, but usually I have little to do in terms of adjustments. I usually feel like these formulas create a pretty good representation of the QBs for the game.
Throwing Power is more difficult. I usually do that more by what I know of the players than anything else. I use the following as a starting point though: Yard per catch*6+long*.1
Throw on the Run is not based on a formula because no stats really support it. I make pocket passers under 70, balanced 71-80 and scramblers 75-up. Again, this is mostly observation.
Play action pass, is much the same. Mostly what I know of a guy. For instance, Boomer Esiason was known for his play action, so he would be rated highly. 2nd string guys end up much lower.
Hope that explains it ok, I will answer any questions you have on the process.