The thing with the tubes is the Radiator. The fan is between it and the case. On the back of the case will be 4 screws or Pins. If you remove them the rad and fan will lower (careful and support the Rad so you dont mess up the hoses)
Between the Rad and the Fan is a adaptor.
Than remove the fan from the Adaptor/Rad and replace with a new 120mm fan.
Oh, sorry, and one more thing do you know what those things are use for in my computer? They are like grills or something on the bottom right side. Not the outside vents, the inner things with screws. Directly unders the HDD
against the mobo wall the preforated metal is for ventalation. Below the HDD is a rack that is made to house more HDDs. The pieces in the sides are rails that other HDDs slide into.