Step 5: Clean up the Copper and Lay Out the Parts
Here comes the first "trick."
Using your perfboard section and the ultra-fine point sharpie, lay out the holes for all your components as you worked them out on paper, In the mirror-image if you made one.
Ultra-fine sharpie just barely fits through the perfboard holes. If it doesn't work on one side, try the other. Worst case -- widen some of the holes with a drill bit.
Putting down evenly-spaced 0.1" dots makes sure that the pads you're about to draw are nicely centered so that your components will fit.