bcp is only used for the delivery of snapshots. For the on-going transactional feed, standard t-sql statements are used (either stored procs or INSERT/UPDATE/DELETE statements depending on how you configure the publication).

If you choose to update the tables being replicated, replication will not bother checking for your changes...i.e. if you update a record on the subscriber and the publisher, you may lose the changes made at the subscriber. If you delete a record on the subscriber and then make a change/deletion to the same record on the published, this may cause a problem that requires intevention since replication will expect to find the record.