I've used different FFPs for a multi-leg tickets many times to maximize earnings. It's usually not a problem, I tend to have my boarding pass reissued with the FFP I am changing to at the airport, to make sure it's in the system. The reason for this is I've had problems with gate agents etc who say they've changed my FFP without actually doing it, so I now ask for a new BP every time.

I'd enter the FFP you want for the first leg in the booking. Then at the connection ask SK to change to EB and give you a new BP.