When you're accompanying Gregorian chant, you have to watch what is the mode of the composition. This because ancient music was not based upon tonality, but modality. There were 8 modes that can be accompained using minor and major chords together. E.g., a gregorian scale could be: d e f g a b-natural c d. What is it? Neither major neither minor but I would use d-minor chords, but, on Gs and Bs I'd play G major, on Es a-minor. Or: g a b c d e f-natural g accompanied with g-major chords but minor ones on As, Ds, Fs. You should also finish in a major chord, expecially if you're finishing with an Amen or Alleluia. If you have gregorian scores to accompany with neumatic notations modes are often written at the beginning of the song; if you have modern notation ones just watch the notes you can see in the score: they simply are the modal scale.
For the registration, try with this simple scheme
If you're playing an Antiphon (Introitus, Offertorium, Communio)
Intonation (Cantor) - till the * : 8' Bourdon
Antiphon (Choir) : add a 4' stop (a flute?)
Psalm (V/): only 8'
Psalm Response (R/) : keep a note (a tenor-related one?) with the pedal (Soubasse 16') to sustain the chant
Gloria Patri (V/)...Sicut erat (R/) as the psalm
Antiphon repeated.
For Mass ordinary: (Kyrie, Gloria, Credo, Sanctus-Benedictus, Agnus Dei, also Ite missa est)
Mass ordinary are often sung "alternatim" with the people.
Intonation (Priest/Cantor): 8' Bourdon
Then alternate 8'+4' / 8'
This does not apply to Kyrie.
Kyrie eleison (Priest): 8' Bourdon
" " (Choir): 8' Diapason/Principal
" " (People): 8' Principal + 4' flute
The same for Christe Eleison and for another Kyrie eleison
The hymns (e.g. Pange Lingua/Veni Creator/...) should be sung by all the choir but, in order not to be monotone, you can alternate a 8' with a 8'+4' in every stanza, but it could be a good idea to sing the Amen with the bigger registration so count the stanza in order to have 8'+4' in the last.
Sequences (e.g. Dies Irae/Veni Sancte/Lauda Sion/Vichtimae Paschali/Stabat Mater) have repeated melodies in their stanzas. Don't repeat two times the melody with the same registration, but be always soft because organ *not should be used* to accompany gregorian chants.