You will only be able to export what is in the top righthand box so you have to lay all your UV's out in the box.You can do this automatically but I would not recommend it ,just select all your UV's and scale them proportionally and then select each individual shell and move them around to fit into the top right square filling it as much as possible with your UV's.

In the UV texture editor under the Polygons menu set click on UV snapshot, choose the resolution your texture is going to be and then save the uv snapshot.
In Photoshop open the Uv snapshot and also your texture file and layer the texure over the uV snapshot which you set to screen mode to see it under your texture.Now you can play with your texture to your hearts content fitting it and sizing it to make the uv's,once done just save your texture file out and then apply it to your model in Maya.