I usually play on Noble level, huge worlds, continents. Like the OP, I tend to be somewhat, ah, expansionist, and I do the "shell game" where I block off entire portions of the continent I'm on with a ring of outer cities and fill in the gaps later. I usually *plan* on taking a hit financially from this expansion, because I've found that by the time I start getting into the late Renaissance/early Industrial period, my finances are back in the black because of the earlier expansion. By 500 AD, I'll usually have 9-12 cities, but my tech spending will be down to 70-80%.
How?
Several things. Cottages, while not *the* end all and be all, ARE very important. Build them early, because it takes time for them to develop to towns. Build them beside rivers, because you get that extra coin per tile, AND if you are a financial civilisation (England under Victoria, Russia under Catherine, etc.) you will be getting three coins right off the bat (1 coin from cottage + 1 coin from river space + 1 extra coin due to Financial trait where any space generating 2 or more coins gets an extra coin = 3). My strategery for cottages is this - build them on plains. Generally, I save flood plains and grasslands for food production, unless I'm already to the point with a city where food prod. is insanely high and it's growing larger than I want/can maintain without stuffing the city with military units to keep down disorder (hereditary rule civic).
Now, one other thing I do is MASSIVE early exploration. Build some scouts and get out there and explore all over your continent. Find every tribal village you can and walk on it. Scouts get an advantage in goodies from tribal villages. Even explore the useless polar regions on a large continent, even though you'll never be doing anything with them. Usually, there's 3-4 villages in an arctic region of a good-sized continent. More often than not, you will get gold from the villages. I've had upwards of 400 gold by 2000 BC just from aggressive exploration with scouts, even when I have 100% science setting. Recently, I've begun setting my science to 90%, with 10% to gold right at the start of the game. This generates an extra +1 in the treasury per turn, which may not seem like much, but DOES build up over time, and will be very good to have when you need it. I don't find this causes much of a problem in maintain tech parity/superiority, either. These early money-making schemes are important because they will "subsidise" your early expansion. I've had upwards of 700 gold by ~750 BC doing both these things, and this allows you to "deficit spend" when your expansion invariably begins to hemorrhage gold through maintenance. Building markets and courthouses will provide a good slowdown on the treasury loss once you hit the later Classical period, but if you've been aggressive (and yes, lucky) in your exploration, you shouldn't have to drop below 70% science even before building these improvements.
Hope this helps (better late than never, eh?)
TQC