I was wondering if there is any compensation for the father when he has custody of the kids for a extended period, or should the father still have to pay the support to the ex even though the kids aren't there?

The father will have to pay child support for the time the children is with him unless the child support order has a clause otherwise.

Example I had my two boys for six months when their mom left them at her mom and took off. But child support enforcement keep getting the money for over the next 6 months, until I got the support order changed.

The child support is figured out over 12 months. The NCP has to pay the support as it states in the support order. If you have your children full time then go back to court and have the order changed; custody changed support should too. However, If you only have the children for "Summer Break" or a month and they will go back to the CP after that then no you can't stop the support, you have to pay it even though you have the kids.