If you fit a 240mm rad to the inside of the case, then you can't fit an optical drive (though you don't necessarily have to remove the drive bay itself), this basically applies to dual fans too.
You can have a single 120mm fan in the roof section, along with an optical drive, but it's likely to be more hassle than it is worth, as you'll be very tight on space in this area.
Also, the potential gains from installing a fan here in most systems are likely to be very small.
The two CPU cooling solutions that make sense in a Prodigy are 240mm rads (ODD removed anyway) and tower air coolers. Having a 120mm fan directly above a tower cooler means it's going against the general flow direction, and also height limiting you, which might be tricking in installation.
My advice for more or less any Prodigy setup - ditch the two fans the case came with if you want to maximise airflow.
Replace the back one with a quality 140mm fan (unless you are going for a huge air CPU cooler, which will effectively become the exhaust itself) and the front one with a 200/230mm, unless availability is poor, in which case use another 140mm. Those two fans will give you better airflow than most towers with 5+ fans, as everything is fairly close together and unobstructed.