I know you are not using Eagle, but I just tested a board I did last year and put two, SMD components that were on opposite sides right over each other. DRC gave no errors using default Eagle settings. With Eagle, the pads of SMD components change color depending on which the side of the board they are placed. Does Protel 99SE do the same? I would be surprised if default settings for a commercial program did not make accommodation for SMD's on opposite sides of the board.
In fact, in Eagle, once two layers are defined by default, there are no other DRC settings that distinguish between the two sides.
John