What do you mean it doesn't show the system going to the heads? That diagram is exactly what it looks like, and the port on the intake closest to the turbo runs directly to the two heads in the diagram, so I'm not seeing what you're referring to.
It doesn't go to the throttle body either, it goes to the manifold, also shown in the diagram.
The second set of ports that you're referring to just go head-crank-head. It's just used to balance the pressure in each, it doesn't run anywhere else.
There are three separate systems, two of which are shown in the diagram. I've listed the connection points in order from left to right when looking at the engine (passenger side to driver side).
intake-crank-manifold (this line has the PCV valve in it to prevent pressurized air from the manifold from pushing its way back into the crank in boost. This is also the line that causes problems when switching to a blow-through MAF setup, since this line allows the manifold to draw air directly from the turbo inlet)
intake-head-head (this is the one that routes through the hard line attached to the stock TMIC)
head-crank-head (this one is hidden under the manifold, you can't really see it until the manifold is pulled)
Line 3 is only on the EJ25, the EJ20 does not have this one. This is where the extra crank vent comes from when people do a hybrid setup (2.5L short block with 2.0L heads).