You can only get Energy Credits by selling items. Honestly you don't need a lot of them at the beginning so don't worry.
There are also other currencies in the game, such as Badges of Exploration. You get Badges by doing Exploration Missions. These missions are repeatable, and for you they are given by Lieutenant Grall (I believe that's how its spelled). They take place in the Delta Volanis Cluster. Badges can also be used to purchase items.
You can use this sto item list to see where you can purchase the various items and how much they cost.