Hi Namara,
1. Using the integration Flow Designer, Define your map(s) and their relationship ie. data out of map A feeds map B.
2. Define your Unix Server under the Server Option and then assign to your system in the system window
3. Perform a find and replace selecting the path criteria of "Run Time", deselecting "Design Time", you will find your current paths assuming they are pointing to your local drive and replace with your UNIX path where the maps are to actually run.
4. Create a deploy script and very map runtime location and deployment directory on your UNIX Platform.
Good Luck
Bob