If I already filled my taxes, but am doing an amended return, the amount changed in my state but I already received my state return. Will I get that difference?

If you started your amended return following the steps here, your return will be calculated using your return numbers as they were originally filed.  

Any changes you make in the program after starting the amended return will be shown as a change in amounts from your originally filed return to your amended return.

The overall amount refunded or due will be calculated after taking into account the original state refund amount.  Since you received a refund on your original return, as long as the amended return shows a larger refund and not an amount due, you should get the difference between the amount originally reflected as a refund to the actual refund amount from the amended return.