The contents tree layout is stored in the .HHC file
After you have generated the basic .HHC file using EasyHH, you can use the HHW (HTML WorkShop) to change the layout of the books and pages. If you haven't already got the full Help WorkShop you can download it from our download page.
To prevent your newly modified .HHC file being overwritten after you build you need to set the 'Check Overwrite' option for your project using the Advanced Config Settings dialog.