The antibiotics were re-prescribed Friday the 17th ... yesterday?
The headaches you are experiencing may be stemming from inflammation and/or clogged sinuses. Sinus headaches are common of a cold/cough and this condition is known as sinusitis (inflammation of the sinus cavities). The cough may be coming directly from an infection within the lungs and can additionally be aggravated by drainage of the sinus when lying down as this will drain from the sinus into the back of the throat and tends to aggravate the coughing. The best treatment for this is to treat the underlying condition(s) and symptoms.
Coughs tend to worsen at night unfortunately, causing a disturbance in rest and sleep. You may try taking an over the counter cough "suppressant" at night, such as a Tussin. You may look for a "Night-Time" formula, which will additionally help you sleep. You can ask your pharmacist for recommendations for this as well. This should help alleviate some of your symptoms. A saline nasal spray may also help in addition with headaches. Taking a hot shower with steam and/or using a humidifier in your room where you sleep will also help open the airways and loosen mucous within the nasal cavity(s), alleviating the headaches. You can also try steam from a hot pot of water, or steam from a hot shower running in the bathroom.
The antibiotic that you are currently taking may not be sufficient enough, if a bacterial infection is infact present. I would additionally suggest a re-visit back to your primary care physician as to obtain a chest x-ray of your lungs, and further testing in order to determine if infection is still present. If you have a greenish or yellow colored sputum or mucous, this is indicative of an infection, and the only way to treat this properly is to take the right antibiotic for that bacteria. This antibiotic that you are taking may not be strong enough as you are still experiencing these symptoms.
If you have any further questions or concerns, please do not hesitate to ask.