A bypass valve is like a blow off valve, but instead of venting boost into the atmosphere it sends it back into the turbo intake (which keeps the air meter from getting screwed up readings).

Manifold pressure and boost pressure are often different since there is a throttle between the turbo and the engine.

For this reason your turbo could be making boost but if your throttle is closed enough there is less pressure (or even a vacuum) in the intake manifold.

In the situations where this occurs my wastegate opens so there is less resistance to the turbo so it can spool to a higher rpm which will come in really handy when the throttle opens up.

The only thing the wastegate does is limit the exhaust gasses to the turbo so it does not overboost.