Agile vs waterfall. Agile is great for software but sometimes limited when planning out a year ahead and interfacing with other disciplines (like marketing and finance.) We typically use a hybrid approach with dev uses agile with tools like PivotalTracker, but on an executive planning level we can use water fall/ gantt charts, etc. When I use project I never let the app do the scheduling, I do it manually. to start, I list all of the items with only their title, duration and resource. Then I go from top to bottom linking dependencies, so that will push future tasks out to where its parent ends. This gives a pretty good projected estimate. As time goes by, change the duration or end date for competed tasks and the rest should adjust.
Microsoft has alot of template projects on their website, so that might be a good place to start and study how they group/ setup things.
That being said, Project can be a HUGE time suck. In all but the most complicated projects its overhead has not warranted the time investment. I personally track multi-quarter projects via a simple PowerPoint slide and then develop via PT.