No matter what you do, you should try to get the most research per turn. Your Financial Advisor (f4) is your friend. Your Research rate is noted in the upper-left hand corner. Every time you make a decision that increases this number, you are improving your empire.
Ways to improve research:
Increase your science rate.
Build/work more cottages.
Build libraries and monasteries (and later, universities and observatories)
Grow your cities (but not past limits!)
Raise enough gold to cover your expenses.
Expand whenever you can afford it.
Go to war to expand your empire, protect your land, and curb your neighbors.
Tech, tech, tech!!!
This is a rather simplistic way of looking at the game, but it will give you a good focus while you learn the ropes. Sometimes you will have to sacrifice short-term gains for long-term gains. That's fine. Just remember: technology is king! As long as you're taking care of your tech, you are probably doing a decent job.
Perfidious Albion?
Just because you came second in the 17th/18th/19th centuries?
Back on topic: stay at a low level; keep playing; it will click soon enough. Most confusing bit? Little coins aren't actually cash but commerce symbols (used to be called trade in previous civ versions with pretty little arrows).
Commerce can be used for cash or research (science slider determines ratio).
Edit: Another confusing bit. Cottages/villages/towns have no effect on population, they simply allow a tile to grow commerce (think money tree) as long as you've allocated one of your population to work the tile.
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