Reading the past few posts, my experience with DL1 is different from yours - are you using Deadlock 1.31 like I am?
Whenever I've killed off the last enemy unit while taking over the last enemy territory, the game has ended for me. I vaguely recall sending units all over a map to find an enemy unit I missed, but that doesn't happen often since I'm usually good about encircling my computer opponent as the end nears.
When I visit an individual territory, I see the net energy situation on the right side. If I produce 20 energy and use 15 energy, I'm accumulating +5 energy in that territory, so I see +5. But if I zoom out to the overall colony, I only see the net energy of everything put together (all power plants minus all energy consumption).
I believe your opponents have one turn to destroy your game winning CC before you actually win, but generally I scrape away all my enemy's bases so I might be recalling that incorrectly.
General discussion, queries, etc. about Deadlock and Deadlock II.