Automating based on fulfillment type is very easy, you can follow the instructions below:
First of all click on 'Repricing' and then on 'Automations'.
Then click on 'Add a new Automation' from a blank automation.
The trigger you are looking for is called 'Product is FBA' or 'Product is MFN'.
Then you can select the rule to 'Move from' and 'To'.
You can add up to three triggers per Automation so could also select to apply this to other criteria such as quantities under a specific amount.
Our Youtube channel provides a video guide for both MFN Videos and FBA videos.
Merchant Fulfilled (MFN):
Fulfilled by Amazon (FBA):