Short answer - neither.
Top fans are almost exclusively exhaust locations, there are very few exceptions to this.
In a Prodigy however, your front-most top fan (let's call it TOP1) is positioned in front of your motherboard and is mainly going to exhaust air which has just been brought in from the front (without it heating up at all). This means it's at best pointless and at worst it'll have a negative effect on temps due to less cool air getting to the motherboard area.
The rear-most top fan (let's call it TOP2) is slightly more interesting in that it does have potential to add airflow/cooling. The difference is that in most cases it sits perpendicular to the motherboard, rather than parallel. This means it's a lot further away so there is no direct flow from VRMs etc or the ability to pull air from between heatsink fins. You can add a fan here, but in my (limited) testing - it does nothing but add noise. There might be some configurations which benefit from TOP2 (obviously if you are running a 240mm rad you might use this anyway) but these are going to be fairly niche.
The biggest improvements to cooling in a Prodigy are replacing the front+back fans with better ones. The Spectre fans which come supplied are pretty quiet but don't move much air and the front fan has a poor location for airflow. If you are using a closed loop cooler then the rear fan gets removed anyway so it's not a significant concern here. For the front fan, any upgrade in size (140/200/230mm) gets you a much better, central fan location which blows straight across the motherboard rather than against the HDD cages.
To address your SP/AF question. It's not one with an obvious answer. The easy answer is "AF for case and SP for rad/heatsink" but both types of fan have both properties and the greater the resistance (whether it's a dust filter/mesh etc) will gradually increase the viability of higher static pressure fans.