As interesting as the Jones Salvage Yard is Headquarters itself. This was probably the single element that grabbed most readers' attention. The idea of tunnels, secret entrances, hideaways, and cool gadgets appealed to a lot of us readers over the years.
Like I did with the Jones Salvage Yard, I've tried to determine the layout of Headquarters and the secret entrances based on the descriptions in Robert Arthur's books and the illustrations of Harry Kane, since I figure these two were in the best position to know what they envisioned for the series. However, there is a lot more uncertainty in the layout of Headquarters compared to the Jones Salvage Yard due to differences in the writing versus illustration. So there are at least two possible floor plans of Headquarters with numerous variations that can be inferred based on the descriptions and illustrations.
Headquarters was described early in the series as a 30-foot trailer that the boys had hidden among the piles of junk. During the course of the series, there are four entrances that are used by the boys (there is also one entrance that is named but never used in the books).
You can use the links below to see the information I have accumulated. If you see some more clues that will help refine the picture of Headquarters, please e-mail me and let me know.