I have my catch can routed with the lines from the breather and PCV both to the catch can, with a breather filter fitted to the top. This way once it is turbocharged any thing that would blow by through the PCV or breather into the manifold is instead caught in the catch can and then the fumes vented to the atomsphere.
Their are alot of ways to setup catch cans, pretty debatable. Tons of threads on Honda-tech about it. On the B-series people remove casting plugs on the back of the block and run fittings to vent crankcase pressure to the catch can, but to help pull the fumes out they also use a vacuum source that never sees boost, for example the intake tube on your turbocharger. When spooling it is a constant source of vacuum and will never create positive pressure, thus helping evacute the crankcase more effectively.
For more information:
http://www.honda-tech.com/zeropost?cmd=tshow&id=1490117