Aft vs. Center Cockpit
Generally, an aft cockpit is considered safer and more comfortable in rough conditions, but this can gets to be more of a fine point depending on the specific design as boats get larger. In a general sense, most center cockpit boats place the seats at or above the main deck level to allow more room for the passage between fore and aft cabins. This greater height means more motion due to rolling. On the other hand, depending on the boat, the more forward position may have less pitching motion but pitching is generally the less violent of the two motions.
As to safety that somewhat depends on the boat design as well, but it is generally thought that waves over the bows are more frequent and violent (speed of the wave added to the speed of the boat vs speed of the wave minus the speed of the boat in a pooping) and so argueably the center cockpit is more exposed to the more violent wave action.
I personally would choose an aft cockpit for an offshore boat under 40 or so feet.