Troubleshoot your heating system by listening for sounds of gurgling in different parts of the water system. You'll hear these sounds through walls when the water pipes in a hydronic system have started to take on some air. If they take on too much air, the heating system will cut out altogether, so don't ignore these warning sounds.
Shut off the boiler fill valves leading to unaffected sections of the heating system, as you only want to fill sections of the piping that need recharging.
Turn on the water at the valve leading from the supply into the boiler, so that it will run through the piping that has taken on air. Just because water begins to run out the boiler drain, though, doesn't mean you've gotten rid of all the air. It may have formed pockets between the boiler and the end of the pipe.
After 5 minutes, turn off the water from the supply, and open the other valves. Listen in the areas affected by the trapped air, to ensure that recharging those pipes drove out the air pockets.