Would we be able to specify a joint custody arrangement in our agreement?

Yes, you may put that in the agreement, if you feel that it is in the best interest of the children. Many courts favor joint legal custody. If you plan to have joint physical custody, you may have a little more difficulty proving to a judge that this is right for the child(ren). Joint physical custody is an arrangement where the child(ren) actually lives with both parents for a specified period of time during each year.

For example;
The child(ren) live with the father each odd month and with the mother each even month. This may seem like a well thought out and negotiated arrangement, but the judge will question whether or not it is a healthy living arrangement. What is great, and content for the parents, may not be best for the child(ren).