At 10-under 132, he is one shot behind the leader, Darron Stiles (64) at the midway stage of the tournament, which is the first domestic stop on the 2013 Web.Com Tour schedule.
Atwal closed with three consecutive birdies and four in his final five after an eagle-3 at the first, which came immediately after a double-bogey at No. 18.
"That double at 18 was kind of exciting," he said.
"It came out of nowhere. I blocked my tee shot right and into the water and then I had to drop way back. I still had 235 (yards) to the pin," he added.
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"I made the putts you're supposed to make today," said Stiles, who is 8-under on the quartet of par-5s.
Boise's Troy Merritt (66), Jason Gore (65) and Ben Martin (67) lurk two shots off the pace heading into the weekend.
Another five players are just three back, including former champion Brett Wetterich (66), who is trying to become the first player in Web.Com Tour history to win the same event three times.
John Daly birdied the final hole for a 2-over 73 and wound up missing the cut by one stroke.
Wetterich is in position to become the first player in Web.Com Tour history to win the same event three times. He is one of 12 players who have won the same tournament twice.