Its MUCH easier to get perfectly placed buttons if you first measure out and sew the button holes.

Then place the buttons in the holes

Line up the button where you want it to be on the opposite fabric and pin it in.

Do this all the way down the garment and then slip the buttons through the holes (unbutton it) and you have all your buttons pined in place!

Now just sew them in and when you are done your garment will close with everything lined up properly

If you are working with buttons without shanks you can also lay the fabrics together and use chalk to mark through the button holes to where the button should be on the other side.