Hello, I'm working on a project with a premade solution containing different projects representing layers :
Business entities, data layer, business logic layer and presentation layer ( at least it's how I understand them ). We have also some class which supposely help us to use nhibernate easily ...

One recommendation made was to use transactions in the business logic layer ( because the data layer wouldn't know if we were in a transaction context or not ), the other was to get the current session and close it in the data layer. Also we use one method / query ( well sometimes it's not exactly like this ) in the data layer.
Is that the right "way" to use nhibernate? Doing any kind of transaction like this is a bit painful ( often some errors, so we have to find workaround...)

I've the feeling that we don't use nhibernate like it should, but I don't have really any experience with mapping o/r tools or plainly "architecture design"/real po knowledge.
In the FAQ, the exemple is "getting session, starting transaction, works, closing transaction, closing session" but should it be in the data or business logic layer? Is this exemple accurate for a 3-tier architecture?

If you are doing a Web app, typically you have one NHibernate session-per-request. NHibernate has its own unit of work, so when you flush the session at the end of each request, NHibernate will synchronize changes made to your entities with the DB.
This is typical usage, but NHibernate lets you control this even more granularly if necessary.
If this is a win forms app, i think you'd keep session as a singleton per thread (correct me if i'm wrong!)

You can get an NHibernate session inside a custom HttpModule if a web app. The session factory is constructed once per application startup since it is expensive procedure.

As far as when to flush/commit the transaction to the db, it depends on your app requirements. I prefer to control when things get persisted and don't use NHibernate's transparent-write-behind functionality, but I know many do. The NHibernate ISession API makes dealing with transactions really simple.

Read Hibernate in Action to get deeper into transaction/session management ideas.