Include Agreements With Divorce Filing?

I have an emergency temporary custody order for our son and we have a signed notarized seperation agreement.

We have been apart for a year and wish to file Absolute Divorce papers this week at the court house.

Do I need to or should I include the custody order and the seperation agreement when I file for Absolute Divorce?

The custody order is already an order of the court and need not be incorporated into the divorce decree. As for the agreement, it depends on the individual circumstances of each as to whether or not I would advise an incorporation.

I assume therefore including the Seperation Agreement when filing our Absolute Divorce papers is not needed or required.

What do you mean by incorporation?

Can you elaborate a little on when you would not want to include the Seperation Agreement along with filing for Absolute Divorce papers?

No, incorporation of the agreement is not required. Incorporation means that the agreement is incorporated into the divorce decree and therefore enforceable as a court order, rather than a contract.
One reason to incorporate an agreement (or not to) depending on your perspective is that alimony becomes modifiable upon a substantial change in circumstances.

So for my perspective with a favorable settlement agreement/contract in hand, which states no alimony to her (due to an admitted and proven affair). I’m better off not incorporating to avoid later court scrutiny and adjustments potentially in her favor?

Based on the limited information I have yes, it would be best not to incorporate your agreement in the decree.