clutchc :
Closed. That is the purpose of the side fans. Is your system running too hot? If so, you may want to try using the rad fans as intake the way the instructions recommend... case/rad/fans.
The 2 side fans are mounted on the sides of the drives in the front . So with the side panel removed , i will still have my side fans mounted like this in the pic
http://www.custompcreview.com/wp-content/uploads/2012/07/custom-pc-review-cm-storm-stryker-review-19.jpg