Start CE then Prototype Game and load ur Save.
Select Exact Value and type in ur EP. (Use standart 4 bytes etc.)
Buy an Upgrade ingame and go back to CE.
Select Changed Value in CE. You should only find 2 Values. Add them to the list by pressing on em twice with left Mouse. Press on the first and then "Find out what writes the Adress" (or something like that). Go to Prototype and play around abit buy an Upgrade or gain some points.
Right Click on the Code and change it to a NOP ( code that does nothing). Then go to ur list and change the Value of the two ones to 12000000 ( BOTH MUST BE SAME !!). Go back to Prototype and see : U HAVE 12 Million EP!!
Note u cant buy upgrades and toggle some Powers on / off. To fix this Problem just close CE and restart Prototype.
Hope i could help some.