There are many ways to earn extra EP in Prototype, however the best way is to complete the main quest. EP gained in each mission depends upon the damage Alex causes to the Military, like destroying a tank or killing the infected attacking him.
The events are also another way to gain EP. If in need of even more EP, collecting the 50 Hint Orbs and the 200 Landmark Orbs, strewn around the city will help earn a huge bonus. 3,201,000 EP can be earned by completing the collections.
In Prototype 2, the bulk of EP is earned by completing missions. Finding collectibles, completing Radnet events and consuming enemies marked with the DNA Consumable symbol will net you lesser, but still substantial amounts of EP. Lastly, very small amounts of EP can be earned by killing or consuming most enemies. Consuming an enemy nearly doubles the EP received, while stealth consuming an enemy almost triples it. However, Heller requires 2,530,000 EP to become fully evolved, so these minor bonuses are basically negligible.
Currently, it is very unlikely that Heller will be fully evolved by the end of the first playthrough, since it would require an incredible amount of time spent grinding for tiny amounts of EP by killing or consuming enemies.