Hi,
I was running this in a lab - worked really straight forward, without any noticeable issues & FCoE (as expected) behaved in the identical fashion as 'standard' FC.
Potentially your FCoE card on the filer side may act as a unified target (both for FC & NAS), but you need a switch supporting this (e.g. Nexus 5k) & ONTAP 8.0.1+
Regards,
Radek