Regarding finances, it often can be wise to crank up your tax rate to as high as it will go without causing "red" public order, below 60%.

Moving the capital closer to low income cities will also aid your income, although primarily through decreasing the income penalties caused by corruption. Building buildings with a law bonus can also help lower this factor - law both removes corruption, and increases happiness at the same time making it the best possible bonus available in R:TW. Temples are generally the best for this purpose since their higher levels can reduce corruption by a huge amount. If you don't have temples dedicated to law bonuses, you may wish to destroy the ones you have to construct them. Ensure that public order is stable first, or you may have rebellious problems while you build them though.

A final note, as Quirinus has said, no city is ever losing you money, regardless of what the display says. Every city contributes to your funds, even if it does seem to be losing money every turn. This is because the game subtracts military upkeep from every settlement before showing its details to you.

Due to this problem, a more accurate depiction of your empire's finances can be seen on the end of turn report. A more accurate depiction of individual cities financial contribution can also be seen, although this requires manual work.

Quite simply, open up the the settlement details scroll, and look at the financial summery. Add up all the items in the "+" section, and then subtract all the items in the "-" section excluding military upkeep. Your result is your city's financial contribution to your empire.

This function can also be used to work out the economic viability of projects in the settlement. Items in the "+" section which are faded out are benefits which will be granted to you by buildings currently in the build que. Items which are gradually fading out constantly in the "-" section are negatives which will be removed by the construction of buildings currently in the build que.

Use this, combined with the cost of each building, to work out which projects are worthwhile for boosting income, and which ones are best left till later.