Using NHibernate 1.2 (latest build)

I'm just starting out with NHibernate (although I am an experienced developer) and I have spent hours poring over the documentation, so hopefully this isn't a dumb question.

I have some complex mappings which don't align too well to a 1:1 table to class mapping, so I thought using a custom loader and sql-* directives in the mapping file would be a good way to deal with this. The problem I found was that in a number of cases, NHibernate would ignore the loader statement and try to construct the sql itself using the class name as the table name (if I didn't provide one).

Are there clear distinctions when the custom loader does or does not apply? I can't seem to find a specific qualification in the docs (or in the Manning e-book I purchased). Any help would be appreciated.

Also, if I am taking the wrong approach to complex mappings, any appropriate design philosophy would be appreciated.

TIA