#1: This is found in a park shed in northern Parker Square. After Hacking the first one, four more ctOS boxes will be marked in the map. You have to reach and hack all of them before the time runs out. It will be better to attempt this with a vehicle handy since you'll be able to move faster and you don't need to get out of the vehicle to hack the box. Just get near enough so you can remotely hack it.
#2: This is found on the railway to the west of Parker Square, near your hideout. After Hacking the first box, the nearest two boxes are behind the building. One needs to be accessed by climbing over some platforms, one is hidden in the corner. The other three are found on the buildings along the street. Use the cameras to find and hack them. The last one is tricky; you have to use the camera from across the street to view the ctOS box on top of the building.
#3:The first box is located on top of the building where the marker is placed. You have to climb the roof of the shop next to it so you can see the box and hack it. After Hacking it, the next box should be nearby while the others are in the marina. The third box on top of the shop is blocked by a gas tank. Shoot the tank with your gun to reveal it. The fourth box is easily hacked by using the camera beside it. Finally, the last box is located in the viewing platform in the marina. You have to vault over the railing to find it.
#4: The box is located on the roof of a garage southwest of your motel hideout. To see it, you have to park a vehicle beside the container van beside the garage so you can climb on top of it and hack the first box. The other four boxes are located in the houses nearby. Two of them are found in ground level, hidden behind some wooden planks. You have to shoot the planks to get them out of the way so you can hack the boxes. The other two boxes can only be hacked via cameras. Find the nearest cameras and switch controls until you get the right angles to see the boxes.