Ty Wigginton, who had all three of Houston's RBIs in their 3-1 victory against San Francisco on Monday while batting second, was moved to the sixth spot in the lineup Tuesday, while Darin Erstad, who did not play Monday, was placed in the No. 2 spot.
Cooper had Wigginton up high Monday because of his on-base percentage against left-handed pitchers -- now .443 -- and he proved that with a two-run single in the sixth and a home run in the eighth.
"Ty swung the bat really well against [Jonathan] Sanchez and had a couple good hits for us," Cooper said. "Tonight, this is a guy [Giants pitcher Tim Lincecum] that's really tough on right-handed hitters, and I need to get my left-handers up there."
Mark Loretta was at third Monday but was replaced by Geoff Blum for Tuesday, and Hunter Pence was given a day off.
Cooper said he had noticed Pence struggling at the plate recently, going 8-for-40 with eight runs in the last 10 games. He struck out seven times in the Astros' four-game series at Cincinnati and went hitless Saturday.
"Hunter works probably harder than most, takes 150 to 200 swings a day," he said. "Sometimes it's too much -- you need less. You need to back up a little bit. So [Monday] I noticed a little bit of frustration.
"You don't want to let the frustration go too far. He's been swinging so good, and I don't want him to go too far to that side. A good day off, relax, maybe go work on some stuff and be ready for tomorrow."
Pence said he does not feel he is struggling, although he said he has had some tough breaks and poor at-bats in the past few outings.
He said he will do whatever he can to correct it, which for him usually means working harder.
"It's all about the feeling in my hands," he said. "Sometimes you have it, sometimes you don't. When you don't have it, sometimes you just have to go in there and battle."
Cooper said he has tried to give each of his players a day off here and there, with Miguel Tejada getting the break last Wednesday.
First baseman Lance Berkman and second baseman Kazuo Matsui are the last two players to get a day's rest, and both have worked nearly every game since the All-Star break.
Krysten Oliphant is an associate reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.