Well, Melgarth, you ain't missin' nuttin! (lol) The manual, though many people refer to it here in the forums, is about worthless. One day searching and browsing through RTW Heaven's posts is worth more than the manual EVER will be. The manual is really just an overly simplified "guide" that really has limited value.
I recommend searching for previous threads on any questions you may have and adding new posts whenever you can't find answers. Everyone here is great at helping.
In short, I find that either the "leave the city, then exterminate the rebels" strategy or going on an aggressive campaign of expansion where you take a settlement every couple of turns can do much to alleviate the problem with shrinking finances while also getting you closer to final victory.
But stagnation (not expanding continually) leads to bankruptcy!
"He said, 'Why should I tarry?' And smiled with tranquil eye; 'In destinies sad or merry, True men can but try.'" Sir Gawain and the Green Knight (Lines 562-565)