Looking at the case specs it says the top has room for either 3 x 120mm fans or 2 x 140mm fans. On account of this I would put the 200mm fan back at the front and have that set as an intake fan.
So now we are left with the 120mm fan that was on the top and the 140mm that was on the rear. Personally I would put these both on the top of the case.
By doing this you would have positive air pressure as you have 2 x 120mm on the bottom and 1 x 200mm on the front as your intake and then 1 x 140mm rear and 1 x 120mm & 1 x 140mm on top as your exhaust. This should be plenty of cooling and as you said you don't need the HDD fan as you have the air from the 200mm blowing over your drives.