A Project is a "container" that can receive several Profiles.
A Profile is something you "create" from the "Mapping Tab" during a cloning or data transfer task, containing ALL details of the task done.
(you can change a Cloning Profile to a Transfer one simply by editing it and un checking the "Clone 2 SQL" OR the "Clone 2 TPS" box in the Source tab)
You can move up or down Profiles within a Project to set their working order when the Project is called from command line argument.