the sub could be how they go through time. and that is why they had to knock Juliet out while traveling there. or the sub is a sub and they just did that because of the effect of going through the bubble (which I also believe is going to a different time dimension ) I just confused myself. 
http://lost.cubit.net/forum/index.php?topic=8484.msg493345#msg493345It's more than likely that the submarine was just a prop.