WBS and Project life cycle

To start a new project for a well known industry you find that we have a ready project life cycle methodology with defined phases and deliverables so you can proceed and build your schedule based on that. On the other hand if you choose to start with building the WBS and follow the PMI advise to build a deliverable oriented logical hierarchy, you will end up with different structure to build your schedule. My questions, is this a conflict? How to proceed? and why?
Thanks