<p>I am starting a normal Java SE project and i am planning to use JPA/Hibernate. I was wondering if anyone could enlighten me as to what is considered the best way to interact with Hibernate in this environment (data access layers)?</p>

I'm not sure what's considered the best approach to this, but at my workplace, we have based most of our Hibernate interaction on these articles:
Don't let Hibernate steal your identity
and
Generic Data Access Objects
They show you how to make your mapped classes in a smart way, and how to implement a generic DAO that can be reused for any persistent class. This has worked out nicely for us.