Simaddict, you are correct. You have to add these lines (or at least the [Effects] line) to the end of the "sim.cfg" in the simobjects/boats/USS_Nimitz folder.
[General]
category=Boat
[contact_points]
static_pitch=0.0 //degrees, pitch when at rest on the ground (+=Up, -=Dn)
static_cg_height=0.0 //feet, altitude of CG when at rest on the ground
[DesignSpecs]
max_speed_mph = 50
acceleration_constants = 0.07, 0.07 //Time constant (effects responsiveness), and max acceleration (Gs)
deceleration_constants = 0.05, 0.05 //Time constant (effects responsiveness), and max acceleration (Gs)
[Effects]
wake = voo_wake_nimitz