Tunnel Two is seen coming up through the floor, while Emergency One is seen in the roof above the desk. Easy Three is most likely behind the green panel on the opposite wall. I base that on the following evidence:

1. Easy Three is most likely on the side of the trailer facing the Salvage Yard, since that entrance is used when no one is looking.
2. The wall containing Easy Three is probably opposite the See-All if we use Harry Kane's illustration on p. 27 of "Whispering Mummy" and assume that Pete is already looking through the See-All at the Salvage Yard and not spinning around getting ready to look at the Salvage Yard.
3. That wall consistently has something that appears to be a drape/curtain of some sort in all the Harry Kane illustrations, indicating something is behind it.

Door Four is most likely on the wall opposite Easy Three (see the diagram of the Jones Salvage Yard to see why this is probably the case); therefore, although it can't be shown on the diagram above, Door Four is on the first wall through which you look to see the rest of Headquarters. On the few illustrations that show this particular wall, there is also something that appears to be a drape/curtain of some sort that may cover the Door Four panel.

The desk and swivel chair are in one end of the trailer, which is consistent with all the illustrations. I have placed the file cabinet on the same wall as shown in all the illustrations, although you'll notice in the illustrations that it seems to move around quite a bit along that wall.