If you could provide a little more detail about the structure of your source document and your requirements, we could probably provide some better feedback.
There are different methods of mapping a source list to a target list. For example, you can simply use a MAP step and allow the IS to perform implicit looping. You can also use a LOOP step and specify the Input Array and Output Array. You can use the append services or indices within a LOOP as suggested above (not recommended for larger lists). Finally, you could also do all your looping and mapping within a Java service.
Which option is best for you would depend on your requirements.