First off, it's YOUR tree, do it however you want to.
Personally I am doing my CHILDRENS' tree. That way I do mine and my wife's all in one go. If you keep your maternal and paternal trees seperate YOU will not appear on either, nor will your siblings, nephews and nieces.
And no, you don't have to make your mind up before you start, when you have entered a few dozen folk you will have a much better idea of whether the style suits what you want to achieve. If not then starting again will not be as bad as starting from scrtch (the research will still hold good). Changing your mind after entering a few thousand people is much more of a bind!
Rob