At many points throughout Ancient Egyptian history they had two capitals. In Memphis, and in Thebes. Was this in order to recognize upper and lower Egypt as different. Was it for administrative purposes? I would understand if they were only regional capitals but they were considered to be national capitals.
Originally, Egypt consisted of two separate kingdoms, Upper Egypt (in the south) and Lower Egypt (in the North). These each had their own capitals. These capitals continued in use through history.
Egypt was ruled by successive family groups known as dynasties. Each dynasty had their own setup. Therefore the capital city of Egypt moved around to a certain degree. For example, the pharaoh Akhenaten established the city of Akhetaten (modern Tell El-Amarna) as his capital in the eighteenth dynasty.
In the Old Kingdom of Egypt, the main capital city was Memphis. After the Old Kingdom, there was a power struggle within Egypt, with the two factions centered on Thebes and Herakleopolis. The Theban faction was victorious, and so in the Middle Kingdom the capital was located in Thebes, primarily.
In addition, the old capitals were treated in a different way from capital cities today. In the New Kingdom period (18th-20th dynasties), Memphis was the capital where the new pharaoh was crowned, and festivals were held, while the government was centered at Thebes, and the ruler lived in his appointed residence city.
But in general, there were many other cities that were used as capitals, and they all depended on which dynasty was in power and what city their ancestors were from.
This is a list of the cities that were used as capitals. As you can see, it varied greatly depending on which dynasty was ruling Egypt at the time.
http://en.wikipedia.org/wiki/List_of_historical_capitals_of_Egypt