Becky, the contents of the New Testament were agreed at the Council of Carthage in 397. A council of Jewish elders had agreed the contents of their Bible (our old testament) in 90 and 118. The Christian Bible that came out of those councils is the one you might call a 'Protestant' Bible today.
The Apocryphal books were always there, on the sidelines, and kept around as being 'possibly of some use', especially as they record Jewish history in the 400 years before Christ. But they came under sustained attack during the Reformation and have had ever-decreasing interest ever since - except for the Roman church, which only decided to declare the apocrypha scriptural as late as 1546, at the Council of Trent. This for me is a big problem with the Catholic tendency to esteem 'Church tradition' so highly. Your own Catholic scholar, Jerome, himself said the apocryphal books should not be included in the Bible - in fact it was he who coined the term 'apocrypha', in order to set them aside from the main body of scripture. So when the Council of Trent decided to formally adopt the apocrypha as scripture, leading to the publication of the Douay-Rheims Bible in 1609, which for the first time scattered the apocryphal books among the rest of the OT, the Roman church really just got its own tradition in a bit of a muddle.
Incidentally, I should clarify, Councils agreed the contents of the New Testament, they did not select them. It seems the books themselves had already entered into wide acceptance in the young church, on their own virtue - something which I consider to be an inspired act of God.
I hold the Bible to be the supreme, reliable authority on all matters of Christian faith and conduct. It records the teachings of Jesus himself, and those closest to him who were inspired by his Spirit to write down things that were useful not just to their original audiences, but to those of us who would follow. What it says about Baptism - just to drag this back on topic ;) - is right from the horse's mouth. Everything God wants us to know about baptism is there in the scriptures, and I believe that the scriptures, when read alone and regarded above any church tradition, modern or ancient, speak very clearly on this topic.
By the way, the apocrypha doesn't say anything about baptism. The only real use of the apocrypha is if you need verses to justify believing in purgatory, or praying for the souls of the dead.