Two-destination packages will always begin and end with a flight: a flight to take you to your first destination and a flight to bring you back from your second destination. You have the option to book a flight between destinations, or you may choose your own method of getting from destination 1 to destination 2.
You may check in to your hotel at any point after you arrive at a destination, and you may also check out at any time before you leave a destination, provided you have satisfied the minimum required stay of one night at each hotel.
If you choose to add a rental car to either destination, it will be picked up at the airport the day you arrive, and returned at the airport the day you depart that destination. If your package involves stays at two different hotels in the same city, your car rental will last for the duration of the trip.