What size parallels should I use?

You should select two parallels of the same height which allow the top surface of your part to exceed the height of the vise. This should be a size that allows you to make all of your passes on the mill without hitting the vise, but not too tall that the part becomes unstable in the vice or that it interferes with the fit of the vise stop- the vise should be holding the part! If the bottom of the part you are milling is uneven, you may need to take a more calculated approach and layer parallels of different sizes horizontally.