Try this experiment
Grab a full bottle of softdrink and with the lid securely fastened flip the bottle over quickly and see if you can get the air bubble in the top to go through the centre of the bottle.

You find you can't?
Then the centre of your header tank, what a great place to put your fuel pick-up to the carburettor. This way it will always be drawing fuel from the centre of the tank and without air bubbles. This gives you a more consistent fuel mixture and stops the motor from running lean (or cutting out) through a series of manoeuvres.

Installing the tank fittings.
If your header tank comes with a clunk of some sort, put it a side and don’t use it. I run the fuel line to the centre of the tank this way it is a little harder for the fuel line to pick up an air bubble. Make sure it doesn’t touch the sides or top/bottom, when the fittings are screwed home in the tank.
The top of the tank should have the vent running to the main fuel tank this should be at the absolute top of the tank or whist filling or you will end up with air trapped in the header tank.

Mounting the tank.
The centre line of the tank can be run in line with the centre line of the carburettor, although I don’t think that moving it too far either way makes too much difference. Try to limit the length of the fuel line too much could cause problems.

Filling the tank.
Place a T type filter in between the Carburettor and the centre pick up in the tank. Making sure that the filter is at the carburettor end of the T filter. This means that when you fill the header tank the crap will flow into the main tank. When the motor is running it is then filtered just before it gets to the carburettor. Whilst filling the tank a clamp should be shut between the filter and the carburettor this will stop you from flooding the engine through the carburettor. Remember when starting your engine to release the clamp before you fire up the starter, or you will run risk of flattening your starter battery and stressing yourself out . A Fuel plug should be used to stop the fuel from coming out after the tank is filled. Make sure you have enough fuel line between the fuel plug and the filter or it can be difficult to pinch off the fuel while you put the plug back in.
The rest of the fuel system is just as normal. The main tank fuel line comes off the top of the header tank and the main tank vent goes to the pressure nipple on the exhaust system.

Header Tank Problems.
If you have found a little bit of uneven ground whilst filling and you have an air bubble in the header tank. Try tilting the helicopter back slightly, so the header tank upper pipe is at the very top of the tank, and all the air should be expelled into the main tank then out the exhaust system. If this doesn’t work sometimes I pulse the fuel in a couple of times, then the bubbles seem to escape fine. If this still doesn’t help your vent tube isn’t at the top of the tank properly and will require fixing.