Well, if you are using AF, then you have to put the focus point over the eye. That means either using the nearest AF point, leave it over the eye and crop slightly, or focus recompose using either the nearest point (for less movement during recomposition) or centre point if in tricky lighting and wanting the best AF (the 5DII being a bit dodgy with the outer points sometimes in low light).
There is no other way of using AF, other than putting a point where you want to focus. If you want to fill the frame you may have to recompose a little, otherwise just shoot a little looser and crop slightly. It all depends on the situation, how much the subject may move whilst recomposing for example and how fast an aperture you are using.