Regarding whether Jenova is controlling Sephiroth or the other way round, Squall of SeeD had made an analysis on the issue in his website.

Unfortunately, the site is closed.

But I remember the conclusion is that both of them had the same goal and is cooperating with each other. (I couldn't remember properly but it is something like this....)

EDIT: I remember reading somewhere that the Sephiroth you faced through out the game is one of his clone that took his form while being control by the real Sephiroth in the Northern crater.