I personally run the engine so the water pump can circulate the water. The thermostat opens at 160f so it only takes about 3 minutes for the water to go through the system. Just fill until it comes out the bleeder on the head before you turn on the engine, then just open the drain plug in the radiator and run it until the water starts coming out of the drain hole then shut off the engine. Repeat once or twice depending on how thorough you are, then refill with Honda coolant.

Also a quick way to bleed the system is:

Using a thin spout funnel that can fit inside the filler neck.

something like this http://www.wayfair.com/Hopkins-2-qt....refid=SS389818

What you do is loosen the bleeder on the head, then just pour coolant into the radiator until it comes out the bleeder, then close it and leave it alone, don't even need to touch the one in the back for this.

Now with the thin spout funnel in the radiator fill neck, and radiator cap off fill the radiator with coolant, put the heater on full blast, then turn the engine on. Now keep filling until there's a good amount of coolant in the funnel with the car at operating temperature(the coolant level drops once the thermostat opens, and also when the cooling fans kick on). What you're going to do while the car is running is squeeze the upper radiator hose, just keep squeezing over and over.

When you squeeze the hose you will see bubbles come out of the coolant in the funnel, this is air. Keep squeezing until no more bubbles come out through the funnel. Watch, when you no longer see bubbles your heater will be so hot it will damn near scald your fingers. Now turn the car off, you're done bleeding, wait about 30 minutes for the coolant to cool off a bit.

You now have two options, wait for the coolant to drain back into the radiator as the system pressure decreases on it's own, or get some towels to protect the electronics, then make a mess and overfill your overflow tank to compensate for the fluid you lost in your mess. Whatever coolant got lost in the mess will be drawn into the system via the overflow so you don't have to worry about getting any air in the system.

Also, after 30 minutes a good chunk of coolant will have drained back into the radiator from the funnel making your mess not as bad.