Baltra is currently an Ecuadorian naval base and is not within the boundaries of Galapagos National Park.
Baltra is one of the entry point into the Galapagos Islands. It was once a North American airbase to protect from enemy attacks. During this period most of the indigenous fauna of the island was exterminated so you should not let this affect your expectations of the Galapagos Islands
From the airport you will be greeted by a guide and showed to buses that take you to where you meet your boat:
To Baltra Harbour: Just a 5-10 min bus ride to the docks and your boat.
To Puerto Ayora: First the bus takes you on a 30 min bus ride to the southern tip of Baltra Island. When the bus reaches the narrow Itabaca Channel, which separates the islands of Baltra and Santa Cruz, you cross via passenger ferry to Santa Cruz, where another bus awaits you and takes you in further 45 min to Puerto Ayora.