Have you ever tried to cross an intersection on a green light, only to find that the road is being blocked by cars that are stuck due to congestion on their lane? Yeah, we've all been there. It's a frustrating thing knowing that the the road ahead is free, yet there are other cars in your way. This is why those yellow boxes, or box junctions, exist.
Those yellow painted boxes indicate an intersection that has traffic flowing from multiple directions. Your car should never obstruct that center space. In short, you shouldn't drive across to the other side unless there is a clear space for you to slot into.
If there's no space, then you simply wait behind the box until there's an opening. Yes, waiting--a concept that seems to be lost on most Filipino drivers, but an important one all the same. This way, you leave the intersection clear for traffic coming from other directions to cross through. This also prevents that situation where the light turns red while you're stuck in the middle. Even without the painted boxes, you should make it a habit to keep intersections clear.
So the next time you see one of these yellow boxes, keep the space free until the traffic ahead clears up. A little patience goes a long way.