I am not clear which of two possibilities you want to do.
1) The simplest is called panelizing. That is, you put multiple PCB layouts on a single piece of PCB copper for etching. In Eagle, go to layers and make all layers show. Then highlight the board you want to copy. Cut or copy it, depending on the version and settings you have. If you are not using version 6.0 or above, use cut. Finally open a new board, I'll call it "panel," and paste the layout you have just copied. Repeat that process with any other board you want to paste on the panel. The key is that the board designs you want to put on the panel are not linked to schematics on the panel. Finally, show only the layers you want before etching, etc. Part numbers will be revised on the panel to avoid duplicates. There are ways around that, but I think that is outside the scope here, since I am not sure of the problem you are having.
2) If you want to electronically link two PCB's, that will be more difficult. Is it because you are using one of the versions that has limited PCB size? If that is the case, you cannot use panelizing, as the panel you have to work with will have the same size limits as you had when designing the board. If it is not a size issue, then you could panelize the boards and draw the electrical connections on the panel.
John