The most straightforward way to do this is to generate matching face meshes on the periodic face pairs. As for the setup of the periodic boundary type in Fluent, you can do this two steps:
1) Make sure to set properly the origin and orientation of the cell zone under Cell Zone Conditions panel
2) You can set up the periodicity manually with Text User Interface command: /mesh/modify-zones/make-periodic and follow the arguments needed to complete the command, accordingly.
An example of this command is: /mesh/modify-zones/make-periodic periodic_a periodic_b yes yes