When attacking while in Cloak mode, you automatically lose all your energy. Instead, go to Armor mode (not Strength mode as this takes up energy when you attack), immediately shoot a soldier in the head, then go back to Cloak mode. They will not see you and you will still have all your energy (and even may gain 1 to 3 %). While you are transitioning to Armor mode, you will have a couple seconds where you are still invisible to the enemy, which allows you to adjust if you are sniping. Even if you reach your time limit that you are invisible after turning off Cloak mode, you can still shoot around and might get away with not being seen as they occasionally panic and move around too much to notice you. You can use this to stay in a stationary location that the A.I. does not touch and easily take out a huge group, (such as the area directly below a watch tower).
To kill Alien Troopers without shooting, when the Alien Troopers jump in the air and levitate shortly doing nothing, they are about to charge at you and possibly kill you in one hit. When they do this, get out of the way. When they charge and miss, there will be an instant where they are idle. Run up to them, grab, and throw them. This may be slightly harder at certain angles. The moment you throw them, they will die (under the Easy difficulty setting at least).
In level 2 "Recovery", under the Delta difficulty setting there is a rocket launcher at the roadblock where there is a truck full of KPA. There is also a rocket launcher and a Precision rifle leaning close to the back wall outside of the house at the radar station. There are at least two rocket launchers at a small white building adjacent to the town hall (KPA HQ). There is a rocket launcher at the gas station cash register. Along with the rocket launchers in the school, those two tanks are easy to destroy. There is also enough Precision rifle ammo at the second floor pillbox of the KPA HQ to max out your capacity.