EntityManager (JPA) shouldn't be mixed with PreparedStatement (
JDBC). JPA is built on top of JDBC, but it uses its own mechanisms.
You should check out javax.persistence.Query and javax.persistence.TypedQuery. Both support parameters in a similar way to PreparedStatement, both with JPA queries and with native queries, although if I recall correctly, native queries are limited to positioned parameters only, and named parameters are only supported for JPA queries.