Do as paratechs says, bleed each register. Also, can you tell us if this noise is constant whenever the boiler is running, or does it only occur when the boiler first fires up, and again when boiler shuts down. Often times, the KNOCKING noise you are hearing is the expansion of copper pipes againts wood joist(caused by being to tight to wood), if this is the case, it will only happen as water is heating, and again when water is cooling. Usually, air in the system will not create a KNOCKING sound, but more just an annoying water air flow sound(cant think of the word to describe it right now, ugh) only at the register.
Basically, turn your themostat way up, let the system run, and tell us if the sound is constant for an hour, or if it is only for the first five or ten minutes, then goes away. If it goes away, turn the thermostat back down, and let us know if the knocking starts again,, if it does, your problem is not with air, but with expansion and contraction of heating pipes against wood surfaces. Hope this makes sense. Lee.