The breather system on an engine carries out two main functions
1) Removal of any blow by gases from the crank case
2) Removal of oil vapour fom the crank case.
This is done to stop pressure building up in the engine which can cause seal failure and/or increased hydrocarbons in the exhaust due to raised oil consumption.
This task is carried out by the breather system and consists of two pipes, one large and one small.
The breathers aim to keep the engine crank case at less than atmospheric pressure i.e. a slight vaccum.
The first breather is the smallest of the two, this is only realy used whilst the engine is at idle or very small throttle openings. This pipe connects to the engine side of the throttle butterfly because under these conditions there is little vaccum on the air filter side. Because the vac at this point in the inlet system is very high and the gas required to run the engine is very small (particularly on tickover), a small pipe is used and often a small controlled drilling (as seen on the V6 breather box or inlet manifold/throttle on the 4 pots) so as to control the amount of gas drawn through and hence idle is not affected (drill the holes out and idle will be affected!).
The larger breather is used on wider throttle openings, at this point the vac in the inlet system is lower the difference in vac on either side of the throttle body is pretty equal and a larger pipe is needed to shift the increased amount of blow by gases. Using a large pipe also results in very little gas passing through the smaller breather pipe under these conditions which, is also a good thing as its less likely to block! This larger pipe is connected to the air filter side of the throttle.
Hope that explains it a bit.