Right, if you bought the plan for the 5 day reservation, you could spread it out over the 5 nights (not 7). However, this can easily amount to 6 days if you check out of resort 1 and move to resort 2 early in the day.
Your credits start the minute you check in and expire at midnight the day that you check out. Thus, if you checked in at 9 am, you could use your credits for breakfast (if desired).
You can check in at any time, but your room may not be ready. They will hold you luggage for you and issue a KTTW that gives you dining and park admission for the day (if you purchased these). Then later in the day, you call a number that they have provided (from any WDW phone--at Guest services, etc.) and they will give you the room number. Your KTTW will already work when you get there, no need to stop at front desk again.