First, I hope you are using a system with two IDE (PATA) pots on the mobo and know how to connect ribbon cables and set jumpers on disk units for Master and Slave.
But to your actual question: it does not matter. When you use cloning software it should insist that YOU use menu choices to set which device in the system will be the SOURCE unit, and which will be the DESTINATION unit. Make SURE you set these correctly. Of course, both units will have to be installed in the system before you start up the cloning software.