Abilities will be positioned based on their Art - Button Position - XY values. This can be changed in the Object Editor under the Abilities section for every single ability. Note how ultimate abilities like Earthquake have an Art - Button Position - X of 3, this means that they move 3 tiles to the right.
If two abilities share the same position then they will "fight" for that position. Whichever ability appears in the Abilities list first will take priority and shove the others away.
X,Y values:
0,0 is the top left, 3,0 is the top right.
1,1 is the middle left, 3,1 is the middle right.
0,2 is the bottom left, 3,2 is bottom right.