To start with you have somewhat of a complex multizone system with a combination of baseboard and radiant heat. A three story also complicates the situation since you have to run a high water pressure.
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You did not mention your water supply system. Is it a well or city service. I have a 1000gal holding tank and haul city water
The reason I ask is for the amount of oxygen entrainment and how long it will take the heat system to get the oxygen out of the water so it can be vented out of the system. When you do a first time bleed after adding large amounts of fresh water you will get most of the air but after the water heats up there will be additional air/oxygen that will be driven out of the water and that also has to be eventually gotton rid of by another bleed. This is why a good auto bleed is important and also why they sell pump isloation valves to prevent the water loss to start with.
In the perfect world there should be a auto vent on all circuits at the highest point to vent the air as it shows up but for some reason you may not have that. So here is what I propose.
Remember at all times you have to keep the water feed pressure up to the operating system normal level during bleeding. You said something about the fact that the auto fill was not working.
I had a circulating pump go out and had it replaced last week, the contractor said that we had a lot of air in the lines and opened a valve from the hot water heater to fill the lines back up with water (this valve is suppose to automatically do this but for some reason did not).
The valve that is not working should be replaced or someone is going to have to hand feed the system while you are bleeding since a drop in pressure can really mess up a system bleed especially if it is a 2nd or 3rd floor problem.
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Try and locate the hose bib connection for each zone that is not working. I just have one hose bib on each side. I can turn off all the valves for each line that are not affected, would this work ok?
Attach a drain hose and set it up in a way so the hose is in a bucket.
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Fill the bucket with water and put the hose in the bucket.won't water come out as well? a bucket would over flow?
Now when you bleed using the hose bib you will be able to see when the air stops bubbling in the bucket out of the zone you are bleeding. In other words no bubbles for a few minutes usually means there is no more air in the system. I usually do this two or three times for a few minutes each time just to make sure no more air bubbles show up in the bucket full of water that the hose is in.
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I hope this work can be done in the basement where the water will not make a mess. Yes it is in the basement with a concreat floor
I have another tool that I made just in case the water can cause problems and that is a sight glass with hose bib connections. It is the same operating principle except you watch the large sight glass for signs of bubbled but the water flows through the hose to the outside of the home.
Try bleeding it in this fashion first to see if you have success. Remember three bleeds minimum and more if air still shows in the bucket.
You can isloate all the lines except the one you are bleeding if you wish since this might increase the flow on the line you are bleeding.
Boiler systems are complex and eash one is different so it is impossible for me to know exactly what to tell you to do since I cannot see exactly what is happening but this will give you a start. If you are on a well system with a pump you will usually have more air entrainment that with a city water supply and it will take a bit longer to get out the residual air after the system is up to temperature.
Keep us posted on the situation.
