Hi Cherity,
Disney has thought of families like yours, because they offer what they call Magic your Way ! You can add park tickets to any resort reservation, and use them however you wish! With the Magic Your Way base ticket, you can pick and choose which theme parks you would like to visit. This ticket allows you to visit one Disney theme park of your choice per day (for the number of days purchased).
For example, if you are staying for three nights, you could add a two day Magic Your Way base ticket and this would allow you to visit either two different theme parks, or you could visit the same park both days.
If you do purchase a package with resort reservation and theme park tickets, you will also be eligible to add the Disney Dining Plan, you can check out more information about it
here.
I hope this helps - have a great trip!