You will see the top ones more than the bottom ones, so mark up and drill the pilot holes for those first - the end ones (E and G strings) all the way through, the A and D ones partway. Then draw a line between the two rear holes and measure off where the A and D string ferrules should sit. Then drill the pilot holes for those from the back partway through as well.

Drilling vertically is key here.

The holes should hopefully at least meet partway through in the middle, and the hole can be opened up a bit if necessary so you can fit a string through. This should leave you with two neat lines of ferrules (even if the rear line might be slightly off from the ideal line, it looks better if the ferrules are all in a neat line).