1) Application Servers implements the specification and while releasing their servers they will be providing the details of their implementation. For a reference please look into this link, which specifies the various JSR implemented by JBOSS 7.
2) When we are just using any implementation provided by application server, then the instance will be taken from the implementation provided by server. Whereas if we have overrided a class then our overridden class will be provided on our operations.