They would be 2 seperate reservations. For each you will have to meet the requirements of
free dining, and this year, that means buying at least 2day park tickets for everyone on the reservation. This could erode the savings of the free dining pretty quick. (If it's 3 nights, you'd average about 120$ savings per adult for FD, while spending about 150$ per adult for the tickets)
You could book the WL portion with a room discount (There's a 40% on deluxes during the same time period as free dining) and choose to buy the dining plan if you wish, though you'd still have to buy 1 day park tickets for each person (requirement for dining plan) for the 2nd reservation, which would cost about 80$ per person.
Lastly, you could book a room-only with the same discount above for the 2nd stay, and just extend the first stay's park tickets to cover both portions. This would leave you paying OOP for meals though.
Depending on how you're planning to eat, either the 2nd or the 3rd would be the best bet.