Okay, in that case you would do a split ressie, and only have
Free Dining for the first two nights, and then the code for the remainder of the stay. There is no way you could make it one reservation and split the deals over the trip (make sense?).
Might be a good way to save some cash... do FD for two nights, get your character meals on those days, then just pay out of pocket while on your room-only deal. You can upgrade your park tickets from your free dining ressie to cover enough days for the full trip once you are at Disney.
However... the free dining for the full trip is going to be the better deal.