So let me try and clear this up as there seems to be some confusion. If you are going to keep your PCV system as a closed system, no breathers, you need to put the catch can on the side with the PCV valve. In a normal system closed system the engine opens the valve and draws crank case blowby using manifold vacuum. On the 4.6 it's the driver's side and I guess on the 5.4 it's on the passenger side. Now with that said, once you open up the system to the atmosphere you are no longer operating the system on manifold vacuum but just venting it as pressure builds. This reverses the flow. Without any vacuum, the PCV valve side will never open up and everything flows out of the passenger side.
So, if you're just installing an inline catch can it needs to be on the driver's side for a 4.6.
If you are utilizing breathers and venting to the atmosphere, you need to install it on the passenger side, or both sides if you remove the PCV valve. If you are opening up the system you should remove the PCV valve from the driver's cam cover and use an oil breather cap. This will allow the crankcase to breath a little more freely than just the little 3/8" outlet and you won't get any oil drippage or spray than if you just had the one outlet.
I don't have part numbers but you can look up the filters by style and size on the K&N website. One has a 3/8" bottom and the other is a 5/8". The oil cap breather is from Central Florida Motorsports and has a ball/check valve in it.
side note: if you are running an induction system where there is boost present in the manifold where the PCV line attaches it kind of fubars everything. Under boost, your PCV system may run backwards. See, in a normal NA set up there is always vacuum present in order to flush the crankcase gases as they build up. If you are running a turbo or centri, under boost, the PCV valve can no longer operate and as the pressure builds in the crankcase it will vent out the intake side. With a roots or twin screw you still have vacuum at the PCV connection because the boost is produced after that point. So at the minimum, if you are running a centri or turbo I would definitely get the CFM oil cap breather if you are leaving the PCV system intact. The ball/check valve will allow your PCV system to run as intended and will allow excess crank case pressure to be relieved when there is no vacuum present to open the valve. But I always suggest to those that are running a turbo or centri to just run 3 breathers.
side note 2: If you do decide to run breathers instead of the standard PCV system you need to increase the frequency of oil changes. Breathers do not run as efficiently as the PCV system in remove crank case blow by gases. I do not mean there will be any pressure build up, but you are not introducing clean air to flush the crank case. What happens in this situation is more fuel and contaminants get dissolved into the oil and the viscosity breaks down quicker. But it's a small price to pay for not running that crap back through your engine.
Hope this helps clear up any confusion and answers some questions.