As long as the multiple copying did not change the size, you will be ok. Many times, I have found the size to be distorted after copying only one time in a copier. You did not mention the method, but I will assume photo-etch.
In this case, match up the two transparencies to be sure they are perfectly the same.
One method (best):
Punch two holes in the pc board and in the transparencies where you will have mounting screws on one side and use these as a guide. You can insert a small piece of wooden dowel to register the two transparencies to the pc board.
Another method (second best): Tape the two pieces of the transparency together on one end and, after you are sure they will match exactly, slip the pc board into the sleeve and place it between two sections of the glass for the photographic process.
In case you are wondering, in a process where you use a silk screen to image the board, the copper clad is normally drilled on a CNC machine first, then the silk screen image is registered to the hole pattern.
In either of these methods, note that you will have to use short pieces of wire where there are vias and you will have to solder these and the component legs on both sides of the board. This is because one side of the board is not electrically connected to the other side of the board like a through hole plated board from a board house. You will not be able to make through hole plated boards without a much more complicated process.
MP