[Fyron]

If the second fan is on the front of the case, you will probably get better airflow with it sucking air in, and the back fan sucking air out. Easy enough to check the temperatures and compare.

The goal is to get air moving past the heat sinks and hot devices. You've got to take heat away from them. If the case is off, the case fan on the back is no longer doing much of anything, since it is not necessarily moving the hot air coming off the CPU, but just air in general. This is not to say that your computer will always run cooler with the case on, of course. It all depends on the setup and the ambient room temperature and humidity.

Poor ventilation (from crappy fans or poor case design overall) will generally increase the temperature inside a closed case from not having enough air moved around.