I attend the byzantine liturgy for time being and I am wondering what this prayer is supposed to mean. After the priest says "Holy Gifts for Holy People" the faithful respond "One is Holy, one is Lord, Jesus Christ, to the glory of God the Father.  Amen."  What is this supposed to mean? Does it mean only Jesus is holy? If so how come the liturgy calls the Holy Mother of God the Holy Theotokos too? Does this prayer imply Jesus but no the rest of the Trinity is Holy? Why are the people called holy before this is said by the faithful? I am asking this just because I am not sure what this prayer is supposed to mean. Thanks you for answering in advance and God bless.

I would suggest to ask www.traditio.com

In the area of Phoenix, the byzantine church changed its missal booklets.  That was in 1995 about.  So, take that into consideration.  Byzantine is changing its rubies and such.

Eastern "Orthodox" say the prayer like this too so I doubt it is a change in rubrics

Booklets change because they are essentially missals meant for the laity. The priest uses a Liturgical book for the liturgy with official liturgical text.  Every order of clergy has their own book which contains their part of the liturgy or office. Any book that the faithful use is not used for anything at the altar

If the liturgy is saying only one of them in the room is Holy, how come the people are called holy? Why does the Church call other men holy if this is true? The divine liturgy calls the church fathers "holy fathers" and in the roman rite there is a response where men are called holy. Then the church also calls the Holy Family the Holy Family. What kind of holiness is this prayer talking about?

It's just praising God, i.e "none of us are holy compared to God". It's not meant to be some sort of dogmatic statement that you can only call God holy. 

I would suggest to ask www.traditio.com

In the area of Phoenix, the byzantine church changed its missal booklets.  That was in 1995 about.  So, take that into consideration.  Byzantine is changing its rubies and such.

No, not really.  Just minor changes, mostly in terms of melodies.  These are immemorial expressions in the Divine Liturgy going back to the Church Fathers and before.  Greeks just always had a more mystical language of theology than the Romans did, who were more legalistic and precise.  Latin is well suited for precise doctrinal definition, while Greek for lofty mystical expression.

TRADITIO.COM, run by some dubiously-ordained "priest," characterizes the 1962 Tridentine Mass as HALF Novus Ordo, which is preposterous, so I wouldn't seek their advice.

Missalettes that state do not kneel, during canon, consecration, after receiving Holy communion, and kneelers taken out. Is that considered minor changes?  That is what happened at St. Stephens' Phoenix.

I spoke with one SSJK (Society of St. Josaphat - Greek Catholic priestly fraternity which cooperates with SSPX) priest and he told me that it is OK to go to such "delatinized" Liturgies (i.e. it is not substantial change in the rite itself), but that it is better to follow the older custom of kneeling during certain times of the Liturgy, since the "delatinizations" were often done due to false ecuмenism with EO (actually, "delatinizations" were never legally enforced, so I don't think it will be considered "illegal" to kneel). In some places (in Ukraine) it was even a custom (and still is in SSJK) to kneel for Communion.
However, if in certain place kneeling hasn't ever been introduced (such as in certain parts of Russia), then one, of course, shouldn't kneel.
I think that if person doesn't know whether kneeling has been introduced in the past in his territory, he should follow the congregation (since it could appear foolish to insist on kneeling if you don't even know whether it was ever "a thing" in this province).

Kneeling is never done on Moryono days. The council of Nicea contains canons forbidding kneeling on Sunday. Eastern Catholic churches follow the canons of their particular churches. In Syriac churches it is forbidden to kneel from first vespers till second vespers or 6pm on Sunday if not attending vespers on Sunday.
In East Syriac churches kneeling is done depending on the altar. Many altars are elevated and in that case only standing can be . In the picture is an Armenian altar. The faithful come to the front of the altar step and the priest communes them by stooping over

Missalettes that state do not kneel, during canon, consecration, after receiving Holy communion, and kneelers taken out. Is that considered minor changes?  That is what happened at St. Stephens' Phoenix.

 
Yep.  Traditionally kneeling was not done in the Eastern Rites, but a combination of standing and bowing.  In fact, in older Eastern Rite churches there are no pews at all, just open space for standing.  There was no sitting either.  In Western countries, kneeling was introduced due to influences from the Roman Rite.  So they rolled these back and reverted to the Eastern practices.