Joe, Ephesians 4:5 emphatically states there is only one baptism not two. And you are right there is more to the question as you stated but we can know God's truth because God is not the author of confusion but of peace and there is peace in knowing God's truth. Remember, God is a God of light and truth. The confusion comes from not rightly dividing God's word.
1 Corinthians 14:33  For God is not the author of confusion, but of peace, as in all churches of the saints.
1 John 1:6  If we say that we have fellowship with him, and walk in darkness, we lie, and do not the truth:
7  But if we walk in the light, as he is in the light, we have fellowship one with another, and the blood of Jesus Christ his Son cleanseth us from all sin.
Therefore leaving the principles of the doctrine of Christ, let us go on unto perfection; not laying again the foundation of repentance from dead works, and of faith toward God,
2 Of the doctrine of baptisms, and of laying on of hands, and of resurrection of the dead, and of eternal judgment.
3 And this will we do, if God permit.
If we back up a little to Hebrews 5:13-14 that gives us the answer to the scriptures you gave in Hebrews 6:1-3
Hebrews 5:13  For every one that useth milk is unskilful in the word of righteousness: for he is a babe.
14  But strong meat belongeth to them that are of full age, even those who by reason of use have their senses exercised to discern both good and evil.
Hebrews 6:1  ¶Therefore leaving the principles of the doctrine of Christ, let us go on unto perfection; not laying again the foundation of repentance from dead works, and of faith toward God,
2  Of the doctrine of baptisms, and of laying on of hands, and of resurrection of the dead, and of eternal judgment.
3  And this will we do, if God permit.
it states everyone that uses the milk of the word and a good example of that is having two baptisms when it states one. That thinking goes against God's word of one baptism, when we see two baptisms, hence being unskilled in the word as it says in verse 13. For that matter anything man devises for doctrine is most always contrary to God's word we are to avoid them.
Romans 16:17  ¶Now I beseech you, brethren, mark them which cause divisions and offences contrary to the doctrine which ye have learned; and avoid them.
18  For they that are such serve not our Lord Jesus Christ, but their own belly; and by good words and fair speeches deceive the hearts of the simple.
When we walk in the light as He is in the light by rightly dividing his word {2 Timothy 2:15 1 Corinthians 2:13} we can discern both good and evil just verse 14 says.
Hebrews 6:1 it says: Therefore leaving the principles of the doctrine of Christ, let us go on unto perfection;
Water baptism is based on the principles of the doctrine of Christ. To understand this we must know who is being spoken to and that is the Jewish Hebrews who had been under the doctrine of Christ which would have been the law and its ordinances. One of those ordinances was water baptism a Jewish ceremonial baptism for Jews who believed their promised Messiah was coming they prepared for it by being water baptized because of their repentance.
Matthew 3:1  ¶In those days came John the Baptist, preaching in the wilderness of Judaea,
2  And saying, Repent ye: for the kingdom of heaven is at hand.
3  For this is he that was spoken of by the prophet Esaias, saying, The voice of one crying in the wilderness, Prepare ye the way of the Lord, make his paths straight.
Matthew 3:11  I indeed baptize you with water unto repentance: but he that cometh after me is mightier than I, whose shoes I am not worthy to bear: he shall baptize you with the Holy Ghost, and with fire:
John's physical water baptism was for repentance only, and never was connected to salvation but it was for those Jews who were repentant of their sins and allowed John to baptize them as a public show of belief of their Messiah soon coming. And as John correctly stated Christ baptizes with the Holy Ghost and fire.
That is why Paul correctly stated in Ephs. 4:5 there is only ONE baptism for a believer and that baptism is spiritual. The word baptism means to immerse or put into and when a believer is baptized by the holy spirit by faith only, he is immersed in into Christ and the one true church that is his body and all believers are living stones that make up this church. 2 Peter 2:5.
God himself adds the members and you can't join it like you a sectarian church this is in competition with the one Christ's is building. Acts 2:47
In this present dispensation that we are in which is the time of the Gentiles {Romans 11:25} the physical acts of worship of Israel does not mix with the worship we have with God today for both
Jew and Gentile is now a new creation in Christ {Ephs 2:15, Galatians 3:28, 2 Corinthians 5:17, Galatians 6:15} in Christ that worship in spirit only.
Philippians 3:3  For we are the circumcision, which worship God in the spirit, and rejoice in Christ Jesus, and have no confidence in the flesh. {You have to use your flesh for water baptism.}
I don't know how it can be any plainer than that. I don't understand why people want to make water baptism a Jewish ordinance a part of their religion when God wants us to be concerned with His Holy Spirit baptism. Even John wanted Christ's baptism when he asked Christ what do you want my baptism for, when I need yours? {but Satan loves it when he gets our focus off of Christ's free spiritual baptism and our eyes and thoughts on a baptism that doesn nothing more then get us wet}
Matthew 3:13  ¶Then cometh Jesus from Galilee to Jordan unto John, to be baptized of him.
14 ÂÂ
But John forbad him, saying, I have need to be baptized of thee, and comest thou to me?
15  And Jesus answering said unto him, Suffer it to be so now: for thus it becometh us to fulfil all righteousness. Then he suffered him.
Christ was water baptized to fulfill all righteousness, His last act of keeping the law. Otherwise if Christ hadn't keep the law He couldn't have healed on the Sabbath or he would have broken the law Himself. But Christ kept the law for us because we can't keep it perfectly. But our faith in Christ and his dying for our sins gives us Christ's perfect righteousness in the new man or new creation that we become
when we are born again spiritually. So that is why it says in
Hebrews 6:1, Therefore leaving the principles of the doctrine of Christ, let us go on unto perfection;
I hope that makes some sense to someone.
tomlane
You have old me that in reality you are not baptized yet (You did a ritual of which you had no understanding, at some time before you were saved ) Nobody has been building baptism into anything here, but we are to be obedient.
speaking of baptism) for thus it becometh us to fulfil all righteousness.
