Yes, you can but they will have to rebook it as a Disney package and you must buy some sort of MYW tickets with it (tixs can be one day or up to ten days). Ticket lengths do not have match how long you are staying on-site.
For example, I booked a split resort reservation, 2 days in Poly and 2 days in AKL, then we are staying off-site for 7 days. I had the postcard pin code special for Poly and AKL stays. I called back to 1-800 disney and was lucky to get a good CM who said I could switch to the package and keep my discounted room rates. The problem was the ticket issue. So she did some computer adjustments to link my two separate room reservations and attached dining for 4 nights, 10 days nonexpiring MYW tickets for Poly stay, and 1 day expiring MYW ticket for AKL stay. (I wanted the 10 days nonexpiring which I can use at a later date). I had to buy two separate sets of tickets because I was staying at two different resorts.
Good luck. The dining plan is a great deal for us because we have a 5 year old (only $10 per day) and 15 month old (so she eats free at the buffets). We can take our time to plan to eat at nice sit down meals and do disney at a relaxed pace rather than commando style. We have PSs for Kona Cafe, Boma, Concourse Steakhouse and Chef Mickey's.