Create a new field called
ItemAlreadyCopied - make it a choice field, with the values Yes and No. If you like, you can set the default value to No.
Then, after your existing line:
IF Current Item:FE1 is not empty Copy Item in Current Item to FE2
ItemAlreadyCopied to Yes.
This will stop it creating duplicate records.
Ensure you understand how the Workflow Start Options affect a workflow. Another solution for you would be to modify the start options so that your workflow only runs once - when a new item is created.
You might need to add to your workflow, or perhaps it is easier to make an additional one, if you want items in FE2 to be updated when FE1 is modified. I would make a separate workflow with the Start Option '...when an item is changed'.