Sidhu,
Yes you can, but as far as I am aware, this is only possible from the Orchestration designer and not the ‘standalone’ mapper.
To use two schemas as your input, simply select two (or more) soruce schemas in the Transform Configuration dialog (which displays when you double-click the Transform shape on the design surface) and the destination schema. When you click Ok the mapper will load displaying two input schemas and one output schema. Build the map as you normally would by dragging from the left to the right to connect nodes.
Regards, Nick.