I'm not an expert with Doctrine - just started using it myself and I have to admit it is a bit of a mixed experience. It does a lot for you, but it's not always immediately obvious how to tell it to do this or that.
For example when trying to use YAML files with the automatic relationship discovery the many-to-many relationship did not translate correctly into the php model definition. No errors as you mention, because it just did not treat it as many-to-many at all.
I would say that you probably need time to get your head around this or that way of doing things and how the elements interact together. And having the time to do things one step at a time would be a good thing and deal with the issues one at a time in a sort of isolation. Trying to do too much at once can be overwhelming and might make it harder to actually find the place something is going wrong.
