Short answer is 'both'.
SOP for certification flight testing is that the FAA pilot is in the Left seat and and a Boeing Flight Test Pilot is in the Right seat. There will generally be at least one other FAA observer on board - typically in the left side observer seat (the right observer seat is normally occupied by the Boeing Flight Test Director). Other observers (both Boeing and FAA) will be in the back monitoring whatever instrumentation that have installed - or crammed into the back of the flight deck during specific test conditions (obviously everyone needs to be seated and strapped in for takeoff and landing or any test conditions which could result in excessive aircraft upset.
There are some pretty major insurance and liability implications if there isn't a company pilot in one of the pilot seats - I've never heard of an instance that FAA pilots were in both seats. It's similar when Boeing does remote flight tests using an operators aircraft - there is always one of the operators pilots in one of the front seats.