It's a strange mixture of two different idioms : 'way down' refers to an imaginary list; the further down ie away from the top of the list, the lower your chances of being selected, or of success. 'In the doghouse' means 'out of favour', 'in trouble', usually for something you've done wrong. These two expressions are not normally combined.

In this sentence, "put him way down" means it significantly worsened his situation or standing, especially in terms of how he was perceived or treated. Specifically: * "Way down" emphasizes the severity of his decline in status. * "In the doghouse" is an idiom meaning someone is in trouble, disfavored, or out of favor with others (e.g., coaches, teachers). So, his academic problems made him fall far out of favor with those who judged or supervised him.

"way down in the dog house = a bad place, an uncomfortable position, or a low ranking. :)