Working a tile does not seem to change the ownership of that tile. If the city is conquered, only the tiles the city directly acquired (culture or bought) are transferred to the conqueror.
Placing a city into an area already owned by the player will transfer ownership of the city tile and the initial inner ring of tiles to that new city.
At the higher difficulties, I've found that the only way to win is to play defensively. Siege units, at least one in each city, probably flanked with another siege unit (or two on a border with an aggressive enemy) and some front line infantry is really the only protection.
My second city is almost always founded in an area with a lot of production bonuses (hills, iron, stone/marble, horses/cows/sheep, etc) and focuses completely on producing military for the entire game. If you grow large enough, founding an additional city of this type can be useful, but if you've got around half a dozen cities or less, one is generally sufficient. Have this city crank out units and only build military buildings there (ideally by rushing them, if you've got the cash). Most of the rest of the empire is money- and happiness- focused, although they might churn out disposable units if war is looking inevitable or going poorly.
When it comes to science, pick techs that get you closer to:
- Money production buildings, like the Bank
- Better siege units (trebuchet, cannon, and especially artillery)
- Better front line infantry (musketmen, infantry, mech. inf., etc)
The AI will become increasingly aggressive towards you if they feel your military power is less than theirs. However, they're terrible military strategists. They will send their entire army right to your cities, with no regards to how that leaves their defenses or how positioning effects their chances at survival. At the higher levels of difficulty, this can mean an almost constant trickle of units.
However, they tend to fail to prepare for the bonuses you gain for fighting on your own turf - take these whenever possible, and then turtle heavily when they declare war. After a while, you'll have an army of extremely powerful units (ie, 2-shot per turn siege units with extra combat range, etc) and great generals, which you can use to push the tide back. Plan on cranking out front line infantry units, as they're somewhat disposable. Put a large priority on preserving your high-level siege units, though.
Likewise, if you see a weak neighbor, go after their stuff. The AI gets big bonuses to production, so their cities are going to be better equipped than ones you could found yourself. Declare war, turtle for a few turns while they bumble about ineffectually at your borders, and then steamroll.
Just remember not to completely abandon your own defenses...
Best Answer
To gain strategic resources, they do not need to be worked by your city's civilians.
Rather, you need only to improve a resource tile within your borders with some tile improvement. For iron, these are mines. Make sure that your workers have built mines over all of your iron deposits. Additionally, resources are lost if the improvement tile is occupied by an unfriendly unit or if the tile improvement on it is pillaged.
Great people's improvements provide resources (but not yield bonuses) once you have researched the required technology.
It sounds like perhaps you have built a mine on a single resource providing 2 iron, and the other two resources are being worked, but are unimproved.