Resource Units (RUs) are a pseudo-currency used at Earth Starbase for "buying" fuel, modules, ships, and crew. They represent the amount of resources available for The Captain to use in his fight against the Ur-Quan Hierarchy. Because RUs are simply a handy way for The Captain to keep track of resources, and not a true currency which is exchanged for goods and services, everything purchased at Starbase can be "sold" back at cost.
You also get RUs immediately by destroying ships in combat -- the scrap metal will be scavenged automatically. You do not need to convert scrap metal into RUs, because the materials were already refined to make the ship you destroyed. Larger ships will give you more RUs than smaller ships. However, if you run away from combat or the flagship is destroyed, the scrap metal cannot be scavenged (even if you destroyed some of the ships in a fleet), so you will not get any RUs from the battle. You will not get RUs for ships from your own fleet which are destroyed by the enemy.