You have your typical resources of wood, food and gold in the first age. The second age lets you get iron and knowledge. The second age also lets you build saw mills and granaries and forges; you build one of each of these per city and it will boost production in that city, along with econ upgrades there. Farm or fish for food and trade for gold. Key thing to remember is that there are a finite number of jobs going in any one city, you are limited to 5 farms per city (7 for Egypt) and most woods support 5 (plus or minus) and mines about 6-8. Build scholars at universities to gain knowledge. It sounds like you are over producing at one city, just move them to another (on yer bike, Tebbit style)
All major upgrades are done at the library and this is your tech tree as all other unit and game upgrades have a library level requirement.
There are two main things that make the economy complex. First, the cost of units and buildings increases the more you have of them, this is actually quite a good thing because it makes it more efficient to build a balanced army, plus, when your army gets wiped out, just look on the bright side, at least the replacements will be cheaper
The second complication is that the cost of upgrades changes depending on other upgrades. In the first age everything costs food wood and gold because that is all you can get, in the second age, the same things may now require iron or knowledge. Fro example, in the first age you can mass an army of hoplites with just food and wood, but hit the second age and you will need iron before you can make any more of the same unit! Another effect is that science (the yellow library track) reduces the cost of the other library upgrades.
I'm not so sure that build order dominance will prevail too much, sure there will be efficient build orders and bad ones, but because you have to tailor your economy to suit your strategy there will be a lot of variations. I would not be too suprised if a killer strat emerges very soon but BHG have publicly stated that they will support the on-line community and fix game imbalances (credit to ES, they did do that).
Upgrade science because that is the key to unlock the econ upgrades
Build cities, in age 1
Go wood heavy, the early ages need it and you can always spend the extra.
Get caravans up immediately you have 2 cities, remember you need 1 per route between cities.
Temple, the taxation upgrade really helps the gold
Build econ buildings at key cities (saw mill, granary, forge)
University, build as soon as you can and fill with scholars, then build in other cities, as the game progesses you will be glad.
Keep an eye on your commerce caps, don't let them flash yellow for long