The Penguins (2-1) used a 28-point outburst in the second quarter to push ahead, fueled by three touchdowns from Wells to Jelani Berassa. The duo connected on scores of 25 yards, 72 and 26 to grab a 31-13 halftime lead.
Wells finished 16 of 22 and threw his fourth touchdown to Nate Adams in the fourth quarter. Berassa had six receptions for 167 yards.
Martin Ruiz rushed for 108 yards on 21 carries for Youngstown State, including an early touchdown in the second quarter to erase a 10-3 deficit.
Joey Cejudo kicked three field goals for the Penguins.