Then you use polygons. You will find that command in the PCB editor 'Place>Polygon Plane' menu. Filling the unused portion of a routing layer with copper polygons is not the same as using a true "plane" - as I stated above, a true "plane" is a contiuous solid copper layer.
In Protel99SE, first make sure you have defined your board outline on the Keepout layer with a continuous outline. Place and route all components. As a final step, select Place>Polygon Plane. On the dialog that appears after you select the polygon place command, you will choose the layer, net, type of pour, and other connection options. You then draw the outline for the polygon over the board surface. Trace, pad, and object clearances will be done automatically based on the design rules you have set up. The available empty space will be filled with copper.