There's probably some pros and cons to either one, but I can't think of any off the top of my head. You can find many excellent shots that use one or the other. Ricky Welch and Rod Jenkins are two of the better known pro's that shoot 3-under. Byron Ferguson, Howard Hill, Fred Bear, and Bill Leslie all shot/shoot split. Try both and see which one you like better.

On a side note, a bow that is tillered for split and shot 3-under, or vice-versa, tends to be noisier.

Chad