Regulator and charging in a portable device
The 3.4/3.5 Volt Li-Ion cell voltage is not necessarily too tight for sourcing 3.3 Volts, as some Low Drop-Out regulators do mention drop-out voltages of the order of 100 mV at small currents. It would be marginal / iffy, though.

If I were doing this, I would boost to 5 Volts, run an LDO or a buck regulator off that 5 Volt rail to get 3.3 Volts, and separately boost directly from the battery for the 12 Volt rail. That way, the 12 volt boost regulator, which seems to be serving your most current-hungry rail, would not suffer 2 stages of efficiency loss, nor would the 5 Volt boost regulator need to be hefty enough to provide the high current needed by the boost regulator for the 12 Volt rail. 

Also, although there are integrated boost / regulate devices that may serve your purpose, as a parametric search on Digikey indicates, there is advantage in keeping the blocks separate: That way, the heat dissipation volumes of each of the 3 parts, 2 boosts and 1 buck / LDO, could be physically separate and thus more of a distributed problem than a thermal hot-spot.