Godhead theology is one of the thorniest issues in Messianism and you will find within the movement the same diversity of belief as in Protestantism. There is no one single "Messianic" Godhead doctrine. Messianics are Trinitarians (three-in-one), Binitarians (two-in-one), Unitarians (Yahweh/Yah'shua alone is God), Arians (Yah'shua is a secondary god) Modalistic Monarchists (Yahweh wears three hats at different times as Father, Son or Holy Spirit), etc.. When talking to a Messianic, do not make assumptions and be sure to ask him what his theology actually is. It is not my purpose to get into a deep debate on Godhead theology here but simply to share my own belief.
There is no more important a question than: Who is Yah'shua (Jesus)? Is He Yahweh? The Son of Yahweh? Just a good man? I contend that the core doctrine of the Messianic/Christian faith is that Yah'shua (Jesus) is fully Deity/God.
My understanding of Scripture is that Yahweh, our Heavenly Father, is a separate Person, Yah'shua (Jesus) the Son is a separate Person, and the Ruach haQodesh (Holy Spirit) is seven separate female Persons, and all are a part of the uniplural Elohim (God). They are all echad or one. My understanding is, however, that they are not co-equal as Trinitarianism teaches but that the Son, though fully Elohim (God) is in eternal subjection to the Father. For a full exposition of the Godhead doctrine, see the excellent articles, Yah'shua the Messiah (Jesus Christ) and His Place in the Godhead and Trinity.
Was it Yahweh who manifested in the flesh as Yah'shua the Messiah (Jesus Christ)? No, it was the pre-incarnate Yah'shua, Son of Yahweh, of the Elohim who manifested in the flesh. The Bible teaches that the incarnate Yah'shua (Jesus) was both on earth and in heaven simultaneously:
"And no man hath ascended up to heaven, but he that came down from heaven, even the Son of man which is in heaven" (John 3:13, KJV).
"And no man has ascended into heaven but He who descended from heaven, the Son of Man, who is in heaven" (ibid., HRV - Hebraic-Roots Version)
Remember this was the mortal Yah'shua (Jesus) speaking to Nicodemus about Himself. he had both come down from heaven and was talking to Nicodemus as well as being in heaven.
Only the original Hebrew/Aramaic and the majority Greek Received Texts (Textus Receptus) preserve this truth - virtually all other Bible versions have obscured it, especially the Catholic/occult-influenced Alexandrian minority MSS. Only God (Eloah) Himself could be both in earth and in heaven simultaneously, thus proving Yah'shua's (Jesus') Deity.
Yah'shua (Jesus) is not Yahweh - He merely bears His Name - "Yah is salvation". But He is most certainly Elohim (God).