Phrasing is handled in at least two contrasting ways in organ playing, depending on whether you have chosen an articulate or a legato approach to touch.
If you have chosen an ARTICULATE APPROACH in a piece, as you would in much early music, you can use any of the three ways of creating or enhancing an accent:
If you use a LEGATO APPROACH in a piece, as you would in most hymn playing and in much of the music of the nineteenth and twentieth centuries, you cannot generally use the first of those three ways--to DETACH. But you can use a DELAYED ATTACK or can PROLONG the notes that you wish to stress.
When, however, a repeated note occurs within a legato piece, then the timing of the release can be adjusted to strengthen or weaken the accent on the following note.