They're factory pieces and come on 1984 Indy, 1985 GT, 1986 - 1988 GT, and 1986 - 1987 aero SE trim levels.
If the car does not already have the ground effects kit installed then no they do not lay over the stock body pieces.
The lower long piece - that you do not have - attaches to the lower side of the door sill and under the front and rear quarters (where the non-aero pieces attach). To installed that main piece onto a car without them you'd have to completely remove the lower sill piece.
The front fender, door, and rear quarter pieces have holes drilled into them from the factory to accept the studs that secure the pieces from the inside. On cars without these you have to drill the holes, but you would be going off of no readily accessible measure points other that placing the pieces onto the body work and marking where the studs hit.
Most individuals when they secure a ground effects kit usually try to get the accompanying fender, door, and rear quarter skins as well, since this makes installation a whole lot easier.
[This message has been edited by Fiero84Freak (edited 04-07-2014).]