We see these questions a lot.
Some general info first. The dining plans and reservations are not interconnected things. Any guest can make a reservation, even day guests who are staying somewhere else (including your own bed). The dining plans are available only to guests at Disney owned and operated resorts inside WDW as part of additions to their hotel reservation.
The dining plans are based on the number of nights you’re staying in that hotel. So, if you’re checking in on Monday and leaving Thursday, that would be 3 nights. A 3 night regular dining plan will include 3 snacks, 3 quick serve meals, and 3 sit down meals that you can use in any order you wish. If you only have a 3 day reservation, then you get your 3/3/3 at check in and they are all available for your use up until midnight on the day you check out. Most people would use their 3 sit down meals for dinner the night they arrive and for their dinners the next two nights as well.
If you only have 3 sit downs and plan to use two sit down credits on your second day and the third credit on your third day, you will have to pay for any other sit down meals out of pocket. Either that, or you’re going to be having dinner at a quick serve counter on the first night along with lunch on the second day and breakfast or lunch on your third day. And of course, with only 6 meals on 4 days, the odds are great that you’ll be paying for a meal out of pocket, maybe even two.