Quarless took his first head coaching position as the head coach of the Eastern Michigan Eagles for the 1992 football season. Quarless took over mid-season as coach at Eastern after the first four games were coached by Jim Harkema, who resigned mid-season after ten years as head coach. Quarless's team produced a record of 1 win and 6 losses. The lone victory was a 7–6 home game against Ohio University.
Quarless was the 19th head football coach for the Southern Illinois Salukis in Carbondale, Illinois and he held that position for four seasons, from 1997 until 2000. His overall coaching record at SIU was 14 wins, 30 losses, and 0 ties. This ranks him tenth at SIU in terms of total wins and 14th at SIU in terms of winning percentage. 
The athletic teams of Eastern Michigan University were known unofficially as the "Normalites" prior to 1929, known as the "Hurons" from 1929 to 1990, and known as the "Eagles" from 1991 to the present.