Thomas was appointed as Kevin Nolan's assistant in January 2017.
The pair had worked together previously during Nolan's time as manager of Leyton Orient.
Thomas left the Os after guiding their Under 18s to the 2016-17 league title, which they wrapped up before Christmas.
He also oversaw a memorable run in the prestigious FA Youth Cup as Orient reached the third round before succumbing to Premier League side Leicester City.
And the new assistant manager, who aided the development of players like Moses Odubajo and Scott Kashket while at Brisbane Road, hopes to help more talent reach their potential in his role at Meadow Lane.