With what you are experiencing you should be able to account for this within the design interface.
Edit the design, choose the choose the level one then select the item tag. In here you can uncheck the box that applies the margin to all sides equally and set the left or right margins accordingly. It seems that you may want to adjust the left margin to be a negative value, this may help you get the sub menu aligned properly.
If you can post back with some steps that you took to create the menu I can review them to see if I can determine where and when you should be making this change.
