I certainly do not proclaim to be any sort of expert, but this might help others cut down on other research.
Seems to be a hot topic - and some serious conjecture, but these are the summaries I have made. Correct me if I have got something seriously wrong.
Diagrams are taken from multiple sources who beleive their system is superior, so disregard "correct way to..." at the bottom of diagrams - they are just used to explain.
The PCV valve is a 1 way valve to prevent the positive pressure from the intake manifold from entering the valve cover, which would create pressure in the crank case and possibly blow seals. The PCV valve also allows the crank case to vent and release that pressure - hence the 1 way valve.
The pcv valve is CLOSED when: there is positive pressure in the intake manifold (eg a F/I car on boost).
The pcv valve is OPEN when: there is negative pressure in the intake manifold. Eg an N/A car with Wide Open Throttle (WOT), or a F/I car when shifting gears or not on boost.
Here is a diagram of stock setup:

When the pcv opens, the air and gunk is SUCKED into the intake manifold (vacuum), then through intake valves and into the combustion chamber to be burned (bad). This is an active system. Ie being actively sucked/vacuumed out of crank case (engine) and into the intake manifold. making this side more important than non-pcv vent for a single catch can setup. This is confirmed by observations of
When running 2 catch cans (both sides) the pcv side fills up much faster than non-pcv side.
Here is a diagram of pcv side single catch can

Here is a diagram of a dual catch can setup

The non-pcv side (aka hot side, exhaust side, on the right when looking at engine) is a passive vent, therefore not a lot of gunk comes out. A catch can in-line here is only useful if turbo'd due to the pcv spending a lot of time shut (as above).
If deleting the pcv valve and running a catch can with both out ports (pcv side and non pcv side, both on cam/valve cover) leading to the catch can, then there is no ACTIVE scavenging and only passive venting which is an old and innefective system used in the 60's. Active venting also creates vacuum in the crank case which is said to be good for the seals and the engine.
Here is diagram of both outlets going into catch can (passive venting)

Other things to be noted:
Catch can should be located somewhere away from heat to improve the condensing of the gunk, therefore keeping it in the catch can. Steel wool simply put in the catch can is also said to help with this.
On high cornering g forces oil can leak out of both the pcv side and non-pcv side. If not collected properly (ie only having an air filter attached to non-pcv side) it can make a mess. For this reason some opt to block off pcv side completely which MAY (possibly) cause oil contamination with fuel and gunk not getting taken out.
Conclusion:
If engine is naturally aspirated run the catch can on the pcv side, keeping pcv in place and dont vent to atmosphere, but plumb back into intake manifold so that the system can work actively, not passively.
If running forced induction run a dual catch can setup with pcv side as above and non-pcv valve either vented to air or back to stock air intake nipple.
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