indeed that is one of the weak points
here are a few keys that might help:
(you need to be in quad edit mode (M) 3 or 4)
Numpad dirs (8 2 4 6) move texture
Numpad 5 90deg rotate
Numpad 7 9 mirror horizontal and vertical
Numpad 1 3 rotate
press [ to fix texture on a single quad (hold Ctrl or Shift to only fix on a single side)
press = to round textures (useful for large quads)
P - reset texture align to default (try to align based on world coordinates)
O - try to align based on local coordinates
I - align selected texture based on camera (not much useful)
U - set all quads to use the currently selected texture