If you manually increase the city size, do think of two things:
(1) Do I want the city to grow just in population?
(2) Do I want to grow the city in both population, and size?
If (2), then do as Isaac suggests.
If (1), then in public service mode: (a) set map mode to city limits, (b) destroy outside road connections until they're out of the city limit, (c) build some rail line (I use narrow gauge) around the maximum extent of the city, (d) grow city to the pop size you like; now the buildings will level up, and the city won't spread outside of the rail line border you just created, (e) remove this rail line, (f) re-attach outside road connections.