There is a passage that runs from the exhaust ports towards the rear (transmission) side of the head. From there it goes to the electronically controlled EGR valve (M/T HX, CVT HX is vacuum controlled). The EGR is mounted on the intake manifold by the distributor. It goes from the EGR valve through maze like passages, located under the fuel rail on the intake manifold. There is a small passage leading into each cylinders intake runner.
For the 92-00 Civics, the HX and VX are the only trims that had EGR valves (at least for the US). 01+ I think all Honda's had EGR valves.