For individual resources, for sources other than your own city, send out your troops to raid various surrounding areas. Raid farms for food, oil fields for oil, silver mines for silver, mines for metal, and lumber mills for lumber. Any other area can be occupied, but it won’t really provide you with anything. However, this can have good strategic uses by occupying it if you want to make your troops go away so they won’t be susceptible to attacks while your army is building.
If you want to secure more resources from enemy attacks besides just what you can fit in the storage bunker, an easy way to do that is to stop collecting the rewards from the missions that you complete. Go and collect them when you need them for construction or for troop training, but otherwise, let them sit indefinitely and they can never be stolen until they are collected.
If your troops die in defense of your city (not in attacking), there is a chance they will go to the hospital. Upgrade your hospitals, and build more hospitals, for a higher chance at more of your troops going to the hospital when they die. Always try to have backup resources, though, so that if your troops die and don’t get sent to the hospital, you can train new ones quickly.
After you join an alliance, hit the “help” button every time you start a new construction and your alliance members can help you by decreasing the construction time. Do the same thing for them by hitting the “help” button that pops up in the lower right corner of the screen, next to the casino button. If your alliance is too inactive, leave and join a bigger, more active alliance.
Each time you gain an experience level, you will gain skill points that can be used to increase the same skills that the research in the lab can do. Tap your portrait to go to the skill tree, and upgrade skills such as improved construction, higher learning (faster research) and plant whisperer (faster food gains). Improved construction is highly recommended because of the vastly increased construction speed, which makes far more buildings eligible for the 3 minute free speed up.
You can complete daily quests that pop up and regenerate on a regular basis in the quest menu. These earn you every resource plus experience points and other bonuses, so complete them as often as possible to maximize your benefits.