If a child element has been placed then the auto-placement algorithm will place that first and then work out what to do with any child elements that have not been placed.
In this example I have placed
box2 on the grid and also made it span 3 grid lines. The rest of the boxes continue to lay out as before.
See the Pen Grid by Example 19: Auto-placement with a positioned element by rachelandrew (@rachelandrew) on CodePen.