With setting up sync between iBank Mobile and iBank 5 you need to go to View> Show Sync Settings (not File> Set Up Device for Syncing). You can also scroll to the bottom of the column on the left side of the iBank 5 window and click on “Sync Settings” from the bottom of the column to set up sync.

File> Set Up Device for Syncing exists in iBank 4 only. The next version of iBank Mobile will include instructions for iBank 5 too.