There are many different ways to mark your enclosures for drilling, from measuring and marking with a pencil to freestyle marking or even taking a drill it and see approach. After many years of suffering from lopsided drill holes and jacks that came dangerously close to pots and switches, I started printing out drilling templates made in Photoshop.
I have provided for you to download an 8.5 x11 PDF that I use to print my templates. I use a glue stick to adhere the template to the enclosure, making sure to line up the edges as best I can. Then I use a center punch to transfer the desired marking to my enclosure. I like to remove the paper before I drill; I find it peels off in one pull without holes in it.