Oh yeah the case has 3 fans. One large intake at the front, and two exhaust fans, 1 on the top, and 1 at the back near top if I remember.
Fans are a personal preference. so it's up to you.
I'd personally use both. I'd put the cpu cooler either at the rear top, or the roof of the case. And the fan occupying that position, I'd move it closer to the front side of the roof. If that makes sense.