Welcome to the forum. To answer your question, the pictures in ship sets are merely bmps of varying sizes. Any Painting program able to edit bmps should serve fine to make a new shipset. You can import such things as the portraits from any picture. As for the ships, we use Doga L3 mostly to make them.
http://www.doga.co.jp/english/download/
If you have not already, I suggest you read the New members thread. Under
Resource sites and links Atrocities has placed a basic ship set tutorial. The new members thread also has links to such sites as PBW and the New Age shipyards, where you can find new ship sets. Good luck.