First off, disposable gloves are essential.
Polyurethane glue works best in closely fitting, and firmly clamped
timber joints. Whilst it will gap-fill, the foam has no strength. It's
pluses are the strength of the joint where it is well compressed, and
that a good joint is truly waterproof.
Experience will tell you how much to apply. On a good tight joint, you
will get some foam expelled, but you can take that off with a scraper
once hard, and then sand or plane the face - but I would emphasise the
good, tight joint.
What sort of work are you doing wit it?