You can use the hours towards your total time and if the aircraft is in this list as a MPA (Multi Pilot Airplane)
www.jaa.nl/licensing/classtyperatings.html you can also count hours towards your JAA ATPL. However you will not be able to obtain a validation without having the relevant type on your FAA license.
Your hours will sure be recognised and no organisation can take away your experience. However try to fly atleast a minimum of 500h in type.
AD