When looking at recMPG in the depth chart and fatigue and minutes played, does the engine take into consideration MPG average or just real world minutes in a pool for the entire season. I.e. if a guy played all 82 games and averaged 20 MPG, could I rest him for the entire first half of the season and then play him at 40 MPG for the second half of the season without a big stamina penalty or would the engine catch on that he is playing way more MPG than his average? Thanks for all your help.

It's the total amount of minutes played divided by 82.
102% of RL minutes / 82 is the maximum.
Playing a 20mpg player 40mpg, regardless of fatigue, will likely put him in the individual possession penalty, causing him to shoot poorly & turn the ball over more. I suggest reading the guide threads posted in this forum for more on this topic, specifically the one on usage.

Usage / Possession Penalty

In general team building advice

Much appreciated.