Your post doesn't provide enough information such as the specific language of the agreement.
Generally, a separation agreement will contain language that says you release (or give up) any and all claims you have or may have had against your employer up to the date you sign the agreement. Even if there is language that says you can still file an EEOC charge, there is also usually language that says your release of claims prevents you from collecting any damages (money) that you may be entitled to in connection with the EEOC charge. Basically, these types of agreements are designed to pay you some money in exchange for your promise not to seek additional money from the employer. Typically, you can't take the money and then seek additional money by filing a lawsuit or an EEOC charge.
That being said, your obligations will be outlined in the separation agreement. If you are unsure of your rights and obligations, have a local employment attorney review the agreement and advise you. Good luck.
You will need to have the document reviewed by a labor/employment attorney to answer your question. The Confidential Separation Agreement is the key to what you are legally able to pursue. Remember, there is a statute of limitations on filing an EEOC Charge so you will need to act quickly. Good Luck!